Starting phenix.real_space_refine on Thu Jul 2 07:04:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u1t_26305/07_2026/7u1t_26305_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u1t_26305/07_2026/7u1t_26305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u1t_26305/07_2026/7u1t_26305_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u1t_26305/07_2026/7u1t_26305_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u1t_26305/07_2026/7u1t_26305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u1t_26305/07_2026/7u1t_26305.map" } resolution = 3.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 32 5.16 5 C 4440 2.51 5 N 1364 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7574 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1336 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 18, 'TRANS': 157} Chain: "B" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1245 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 15, 'TRANS': 146} Chain: "C" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1336 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 18, 'TRANS': 157} Chain: "D" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1238 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 15, 'TRANS': 145} Chain: "E" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1209 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain: "F" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1210 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Time building chain proxies: 1.70, per 1000 atoms: 0.22 Number of scatterers: 7574 At special positions: 0 Unit cell: (113.52, 131.58, 129, 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 118 15.00 O 1620 8.00 N 1364 7.00 C 4440 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: 0.85 Conformation dependent library (CDL) restraints added in 353.6 milliseconds 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1174 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 6 sheets defined 33.9% alpha, 27.0% beta 54 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.693A pdb=" N SER A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 528 Processing helix chain 'A' and resid 568 through 586 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'B' and resid 475 through 492 removed outlier: 4.019A pdb=" N SER B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 528 Processing helix chain 'B' and resid 568 through 586 Processing helix chain 'C' and resid 475 through 492 removed outlier: 4.030A pdb=" N SER C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 528 Processing helix chain 'C' and resid 568 through 586 removed outlier: 3.515A pdb=" N ALA C 572 " --> pdb=" O THR C 568 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 593 Processing helix chain 'D' and resid 475 through 492 removed outlier: 3.993A pdb=" N SER D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 528 Processing helix chain 'D' and resid 568 through 586 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.985A pdb=" N ASN D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 588 through 592' Processing sheet with id=AA1, first strand: chain 'A' and resid 532 through 533 removed outlier: 5.180A pdb=" N CYS A 560 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 511 " --> pdb=" O CYS A 560 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 504 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 595 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLY B 603 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL A 597 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP B 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 599 " --> pdb=" O SER B 599 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 597 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLY A 603 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 595 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL B 504 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 560 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 538 removed outlier: 5.180A pdb=" N CYS A 560 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 511 " --> pdb=" O CYS A 560 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 504 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 595 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLY B 603 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL A 597 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP B 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 599 " --> pdb=" O SER B 599 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 597 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLY A 603 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 595 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL B 504 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 560 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL B 559 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 532 through 533 Processing sheet with id=AA4, first strand: chain 'C' and resid 532 through 533 removed outlier: 5.102A pdb=" N VAL C 504 " --> pdb=" O PHE C 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 532 through 533 removed outlier: 5.259A pdb=" N VAL D 559 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 532 through 533 removed outlier: 5.089A pdb=" N CYS D 560 " --> pdb=" O GLY D 511 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.06 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: 1312 1.33 - 1.45: 2523 1.45 - 1.57: 3898 1.57 - 1.69: 234 1.69 - 1.81: 48 Bond restraints: 8015 Sorted by residual: bond pdb=" O3' DT E 49 " pdb=" P DG E 50 " ideal model delta sigma weight residual 1.607 1.675 -0.068 1.50e-02 4.44e+03 2.08e+01 bond pdb=" N ILE B 528 " pdb=" CA ILE B 528 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.60e-03 1.35e+04 1.96e+01 bond pdb=" P DA E 21 " pdb=" O5' DA E 21 " ideal model delta sigma weight residual 1.593 1.636 -0.043 1.00e-02 1.00e+04 1.88e+01 bond pdb=" N ASN B 475 " pdb=" CA ASN B 475 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.79e+01 bond pdb=" P DT F 22 " pdb=" O5' DT F 22 " ideal model delta sigma weight residual 1.593 1.635 -0.042 1.00e-02 1.00e+04 1.79e+01 ... (remaining 8010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 9216 1.98 - 3.95: 1812 3.95 - 5.93: 254 5.93 - 7.90: 91 7.90 - 9.88: 2 Bond angle restraints: 11375 Sorted by residual: angle pdb=" O3' DT E 11 " pdb=" P DC E 12 " pdb=" O5' DC E 12 " ideal model delta sigma weight residual 104.00 96.20 7.80 1.50e+00 4.44e-01 2.70e+01 angle pdb=" C4' DA E 19 " pdb=" O4' DA E 19 " pdb=" C1' DA E 19 " ideal model delta sigma weight residual 110.10 105.37 4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" O4' DG F 50 " pdb=" C4' DG F 50 " pdb=" C3' DG F 50 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N THR B 590 " pdb=" CA THR B 590 " pdb=" C THR B 590 " ideal model delta sigma weight residual 114.04 108.31 5.73 1.24e+00 6.50e-01 2.14e+01 angle pdb=" CA GLY A 603 " pdb=" C GLY A 603 " pdb=" O GLY A 603 " ideal model delta sigma weight residual 122.59 118.11 4.48 1.04e+00 9.25e-01 1.85e+01 ... (remaining 11370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 3931 35.82 - 71.64: 527 71.64 - 107.45: 9 107.45 - 143.27: 7 143.27 - 179.09: 2 Dihedral angle restraints: 4476 sinusoidal: 2619 harmonic: 1857 Sorted by residual: dihedral pdb=" C4' DA E 19 " pdb=" C3' DA E 19 " pdb=" O3' DA E 19 " pdb=" P DT E 20 " ideal model delta sinusoidal sigma weight residual -140.00 39.09 -179.09 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA E 55 " pdb=" C3' DA E 55 " pdb=" O3' DA E 55 " pdb=" P DG E 56 " ideal model delta sinusoidal sigma weight residual 220.00 70.89 149.11 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DG E 13 " pdb=" C3' DG E 13 " pdb=" O3' DG E 13 " pdb=" P DA E 14 " ideal model delta sinusoidal sigma weight residual 220.00 80.63 139.37 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 4473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 944 0.127 - 0.255: 164 0.255 - 0.382: 9 0.382 - 0.509: 79 0.509 - 0.636: 30 Chirality restraints: 1226 Sorted by residual: chirality pdb=" P DT E 1 " pdb=" OP1 DT E 1 " pdb=" OP2 DT E 1 " pdb=" O5' DT E 1 " both_signs ideal model delta sigma weight residual True 2.34 2.97 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DA F 3 " pdb=" OP1 DA F 3 " pdb=" OP2 DA F 3 " pdb=" O5' DA F 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" P DA E 37 " pdb=" OP1 DA E 37 " pdb=" OP2 DA E 37 " pdb=" O5' DA E 37 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.41e+00 ... (remaining 1223 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT F 59 " 0.007 2.00e-02 2.50e+03 1.02e-02 2.62e+00 pdb=" N1 DT F 59 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DT F 59 " -0.014 2.00e-02 2.50e+03 pdb=" O2 DT F 59 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DT F 59 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT F 59 " 0.018 2.00e-02 2.50e+03 pdb=" O4 DT F 59 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DT F 59 " 0.008 2.00e-02 2.50e+03 pdb=" C7 DT F 59 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DT F 59 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA F 42 " -0.014 2.00e-02 2.50e+03 8.70e-03 2.08e+00 pdb=" N9 DA F 42 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA F 42 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA F 42 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA F 42 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA F 42 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA F 42 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA F 42 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA F 42 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA F 42 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA F 42 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC E 29 " 0.018 2.00e-02 2.50e+03 8.96e-03 1.81e+00 pdb=" N1 DC E 29 " -0.016 2.00e-02 2.50e+03 pdb=" C2 DC E 29 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DC E 29 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DC E 29 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC E 29 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC E 29 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DC E 29 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC E 29 " -0.004 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2379 2.83 - 3.35: 8955 3.35 - 3.86: 16531 3.86 - 4.38: 18685 4.38 - 4.90: 25868 Nonbonded interactions: 72418 Sorted by model distance: nonbonded pdb=" NZ LYS D 586 " pdb=" O5' DC E 12 " model vdw 2.312 3.120 nonbonded pdb=" NH1 ARG C 538 " pdb=" OP1 DA E 21 " model vdw 2.358 3.120 nonbonded pdb=" NH2 ARG D 522 " pdb=" OP2 DT F 46 " model vdw 2.380 3.120 nonbonded pdb=" O SER C 447 " pdb=" O3' DC E 27 " model vdw 2.397 3.040 nonbonded pdb=" N GLY B 454 " pdb=" OP1 DT E 49 " model vdw 2.401 3.120 ... (remaining 72413 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 454 through 613) selection = (chain 'B' and resid 454 through 613) selection = (chain 'C' and resid 454 through 613) selection = (chain 'D' and resid 454 through 613) } 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.840 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 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 : 0.013 0.068 8015 Z= 0.944 Angle : 1.611 9.877 11375 Z= 1.113 Chirality : 0.172 0.636 1226 Planarity : 0.002 0.010 1071 Dihedral : 24.341 179.086 3302 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 57.86 Ramachandran Plot: Outliers : 1.20 % Allowed : 5.85 % Favored : 92.95 % Rotamer: Outliers : 4.77 % Allowed : 5.32 % Favored : 89.91 % 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: -1.17 (0.30), residues: 667 helix: 1.70 (0.28), residues: 198 sheet: -2.71 (0.49), residues: 78 loop : -1.77 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 486 TYR 0.004 0.001 TYR D 510 PHE 0.008 0.001 PHE D 571 TRP 0.007 0.001 TRP D 503 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.01330 / 0.94 ( 8015) covalent geometry : angle 1.61076 / 1.11 (11375) hydrogen bonds : bond 0.22949 / 15.62 ( 362) hydrogen bonds : angle 12.82478 / 9.46 ( 1014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 5 residues processed: 201 average time/residue: 0.1018 time to fit residues: 26.4509 Evaluate side-chains 98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 541 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS C 480 ASN D 475 ASN D 480 ASN D 519 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.091175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.069611 restraints weight = 31582.165| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.82 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8015 Z= 0.253 Angle : 0.959 9.956 11375 Z= 0.526 Chirality : 0.060 0.316 1226 Planarity : 0.007 0.067 1071 Dihedral : 29.654 156.302 2061 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 26.83 Ramachandran Plot: Outliers : 0.75 % Allowed : 5.10 % Favored : 94.15 % Rotamer: Outliers : 6.06 % Allowed : 15.78 % Favored : 78.17 % 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: -0.89 (0.31), residues: 667 helix: 1.95 (0.32), residues: 212 sheet: -2.78 (0.42), residues: 96 loop : -1.57 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 538 TYR 0.021 0.003 TYR B 561 PHE 0.024 0.003 PHE A 562 TRP 0.027 0.004 TRP A 464 HIS 0.004 0.001 HIS B 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.25 ( 8015) covalent geometry : angle 0.95853 / 0.53 (11375) hydrogen bonds : bond 0.10405 / 6.89 ( 362) hydrogen bonds : angle 6.55213 / 4.62 ( 1014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 563 MET cc_start: 0.7951 (ttp) cc_final: 0.7560 (ttt) REVERT: B 580 LYS cc_start: 0.6929 (mmtm) cc_final: 0.6243 (ttmm) REVERT: C 467 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7703 (mmmt) REVERT: C 605 ASP cc_start: 0.8134 (t0) cc_final: 0.7290 (m-30) outliers start: 33 outliers final: 22 residues processed: 122 average time/residue: 0.0781 time to fit residues: 13.2205 Evaluate side-chains 100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 610 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 50.0000 chunk 69 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 0.0270 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.086085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.064234 restraints weight = 31134.961| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.74 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 8015 Z= 0.213 Angle : 0.812 8.709 11375 Z= 0.456 Chirality : 0.051 0.287 1226 Planarity : 0.006 0.050 1071 Dihedral : 29.407 165.174 2061 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.75 % Favored : 92.95 % Rotamer: Outliers : 6.06 % Allowed : 16.70 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.32), residues: 667 helix: 2.02 (0.34), residues: 212 sheet: -2.67 (0.47), residues: 80 loop : -1.45 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 496 TYR 0.013 0.002 TYR A 561 PHE 0.022 0.003 PHE C 610 TRP 0.020 0.003 TRP B 503 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.21 ( 8015) covalent geometry : angle 0.81174 / 0.46 (11375) hydrogen bonds : bond 0.08445 / 5.64 ( 362) hydrogen bonds : angle 5.78039 / 4.10 ( 1014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 TYR cc_start: 0.7955 (p90) cc_final: 0.7696 (p90) REVERT: B 580 LYS cc_start: 0.7228 (mmtm) cc_final: 0.6547 (ttmm) REVERT: C 495 GLU cc_start: 0.6607 (mp0) cc_final: 0.6278 (mp0) REVERT: C 563 MET cc_start: 0.8219 (ttp) cc_final: 0.7982 (ttm) REVERT: C 605 ASP cc_start: 0.8162 (t0) cc_final: 0.7406 (m-30) REVERT: C 609 TRP cc_start: 0.7194 (t60) cc_final: 0.6958 (t60) REVERT: C 613 MET cc_start: 0.6868 (mpp) cc_final: 0.5107 (mmt) outliers start: 33 outliers final: 20 residues processed: 105 average time/residue: 0.0629 time to fit residues: 9.6982 Evaluate side-chains 93 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 610 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 5 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 50.0000 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 60 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.084482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.062351 restraints weight = 31610.832| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.84 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8015 Z= 0.187 Angle : 0.773 8.669 11375 Z= 0.433 Chirality : 0.050 0.310 1226 Planarity : 0.006 0.051 1071 Dihedral : 29.289 163.291 2059 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.90 % Favored : 92.80 % Rotamer: Outliers : 4.40 % Allowed : 18.72 % Favored : 76.88 % 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: -0.58 (0.32), residues: 667 helix: 1.95 (0.34), residues: 212 sheet: -2.27 (0.47), residues: 82 loop : -1.37 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 532 TYR 0.008 0.002 TYR A 518 PHE 0.026 0.003 PHE D 562 TRP 0.015 0.002 TRP B 609 HIS 0.005 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.19 ( 8015) covalent geometry : angle 0.77295 / 0.43 (11375) hydrogen bonds : bond 0.07779 / 5.31 ( 362) hydrogen bonds : angle 5.36689 / 3.79 ( 1014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 580 LYS cc_start: 0.7398 (mmtm) cc_final: 0.6808 (ttmm) REVERT: C 495 GLU cc_start: 0.6844 (mp0) cc_final: 0.6216 (mp0) REVERT: C 605 ASP cc_start: 0.8249 (t0) cc_final: 0.7532 (m-30) REVERT: C 609 TRP cc_start: 0.7370 (t60) cc_final: 0.6635 (t60) outliers start: 24 outliers final: 21 residues processed: 98 average time/residue: 0.0683 time to fit residues: 9.8985 Evaluate side-chains 92 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 610 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.081566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.059449 restraints weight = 31097.985| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.73 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 8015 Z= 0.187 Angle : 0.754 8.361 11375 Z= 0.422 Chirality : 0.048 0.311 1226 Planarity : 0.006 0.056 1071 Dihedral : 29.300 155.285 2057 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.20 % Favored : 92.50 % Rotamer: Outliers : 4.77 % Allowed : 17.98 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.32), residues: 667 helix: 1.93 (0.35), residues: 212 sheet: -1.94 (0.51), residues: 83 loop : -1.32 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 594 TYR 0.012 0.002 TYR A 518 PHE 0.020 0.002 PHE A 562 TRP 0.014 0.002 TRP D 503 HIS 0.002 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 ( 8015) covalent geometry : angle 0.75435 / 0.42 (11375) hydrogen bonds : bond 0.07638 / 5.24 ( 362) hydrogen bonds : angle 5.06330 / 3.59 ( 1014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 495 GLU cc_start: 0.7071 (mp0) cc_final: 0.6860 (mp0) REVERT: C 605 ASP cc_start: 0.8278 (t0) cc_final: 0.7650 (m-30) REVERT: C 609 TRP cc_start: 0.7616 (t60) cc_final: 0.6951 (t60) REVERT: C 613 MET cc_start: 0.6883 (mpp) cc_final: 0.6343 (mpp) REVERT: D 613 MET cc_start: 0.7550 (mmm) cc_final: 0.6392 (mpp) outliers start: 26 outliers final: 23 residues processed: 99 average time/residue: 0.0495 time to fit residues: 7.3906 Evaluate side-chains 97 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 610 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.0060 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.081765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.059520 restraints weight = 31050.568| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.77 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8015 Z= 0.157 Angle : 0.726 8.474 11375 Z= 0.404 Chirality : 0.048 0.320 1226 Planarity : 0.006 0.053 1071 Dihedral : 29.340 153.165 2057 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.90 % Favored : 92.80 % Rotamer: Outliers : 4.22 % Allowed : 18.53 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.33), residues: 667 helix: 2.15 (0.35), residues: 212 sheet: -1.74 (0.52), residues: 83 loop : -1.27 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 594 TYR 0.009 0.002 TYR B 561 PHE 0.022 0.002 PHE C 610 TRP 0.016 0.002 TRP D 609 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 ( 8015) covalent geometry : angle 0.72587 / 0.40 (11375) hydrogen bonds : bond 0.07143 / 4.89 ( 362) hydrogen bonds : angle 4.84894 / 3.42 ( 1014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 538 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6337 (mtm-85) REVERT: C 605 ASP cc_start: 0.8202 (t0) cc_final: 0.7577 (m-30) REVERT: C 609 TRP cc_start: 0.7556 (t60) cc_final: 0.6801 (t60) REVERT: C 613 MET cc_start: 0.6900 (mpp) cc_final: 0.6097 (mpp) REVERT: D 613 MET cc_start: 0.7469 (mmm) cc_final: 0.6257 (mpp) outliers start: 23 outliers final: 19 residues processed: 100 average time/residue: 0.0637 time to fit residues: 9.3193 Evaluate side-chains 96 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 610 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 75 optimal weight: 10.0000 chunk 57 optimal weight: 0.0970 chunk 65 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.079652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.057510 restraints weight = 30991.795| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.72 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8015 Z= 0.176 Angle : 0.740 8.566 11375 Z= 0.413 Chirality : 0.049 0.328 1226 Planarity : 0.006 0.059 1071 Dihedral : 29.437 171.463 2057 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.50 % Favored : 92.20 % Rotamer: Outliers : 4.04 % Allowed : 20.73 % Favored : 75.23 % 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: -0.36 (0.33), residues: 667 helix: 1.99 (0.35), residues: 208 sheet: -1.67 (0.51), residues: 83 loop : -1.23 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 496 TYR 0.013 0.001 TYR A 518 PHE 0.019 0.002 PHE A 562 TRP 0.016 0.001 TRP D 609 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 ( 8015) covalent geometry : angle 0.74000 / 0.41 (11375) hydrogen bonds : bond 0.07436 / 5.13 ( 362) hydrogen bonds : angle 4.89270 / 3.45 ( 1014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 538 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6944 (mtm-85) REVERT: C 605 ASP cc_start: 0.8288 (t0) cc_final: 0.7713 (m-30) REVERT: D 563 MET cc_start: 0.8001 (ttt) cc_final: 0.7732 (ttt) REVERT: D 613 MET cc_start: 0.7492 (mmm) cc_final: 0.6331 (mpp) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.0602 time to fit residues: 8.7286 Evaluate side-chains 99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 610 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 50.0000 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.080117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.057966 restraints weight = 31285.890| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.76 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8015 Z= 0.153 Angle : 0.723 8.892 11375 Z= 0.402 Chirality : 0.047 0.322 1226 Planarity : 0.006 0.057 1071 Dihedral : 29.503 167.503 2057 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.60 % Favored : 93.10 % Rotamer: Outliers : 4.04 % Allowed : 19.45 % Favored : 76.51 % 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: -0.07 (0.33), residues: 667 helix: 2.22 (0.35), residues: 214 sheet: -1.29 (0.53), residues: 78 loop : -1.18 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 594 TYR 0.008 0.001 TYR B 561 PHE 0.018 0.002 PHE A 562 TRP 0.024 0.002 TRP D 609 HIS 0.006 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 ( 8015) covalent geometry : angle 0.72285 / 0.40 (11375) hydrogen bonds : bond 0.06978 / 4.80 ( 362) hydrogen bonds : angle 4.70587 / 3.31 ( 1014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 538 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6791 (mtm-85) REVERT: C 605 ASP cc_start: 0.8201 (t0) cc_final: 0.7625 (m-30) REVERT: C 609 TRP cc_start: 0.7753 (t60) cc_final: 0.6960 (t60) REVERT: C 613 MET cc_start: 0.6973 (mpp) cc_final: 0.6594 (mpp) REVERT: D 613 MET cc_start: 0.7147 (mmm) cc_final: 0.6075 (mpp) outliers start: 22 outliers final: 19 residues processed: 97 average time/residue: 0.0679 time to fit residues: 9.6343 Evaluate side-chains 100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 597 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 36 optimal weight: 0.0270 chunk 26 optimal weight: 0.0170 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.080186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.058385 restraints weight = 31050.143| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.72 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.7178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8015 Z= 0.150 Angle : 0.727 8.443 11375 Z= 0.403 Chirality : 0.047 0.317 1226 Planarity : 0.006 0.062 1071 Dihedral : 29.525 167.202 2057 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.20 % Favored : 92.50 % Rotamer: Outliers : 4.22 % Allowed : 19.63 % Favored : 76.15 % 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: -0.07 (0.33), residues: 667 helix: 2.13 (0.35), residues: 214 sheet: -0.93 (0.54), residues: 75 loop : -1.20 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 496 TYR 0.009 0.001 TYR A 518 PHE 0.016 0.002 PHE A 562 TRP 0.018 0.001 TRP D 609 HIS 0.006 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 ( 8015) covalent geometry : angle 0.72721 / 0.40 (11375) hydrogen bonds : bond 0.06901 / 4.74 ( 362) hydrogen bonds : angle 4.69322 / 3.30 ( 1014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: B 538 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6751 (mtm-85) REVERT: C 605 ASP cc_start: 0.8257 (t0) cc_final: 0.7663 (m-30) REVERT: C 609 TRP cc_start: 0.7688 (t60) cc_final: 0.7051 (t60) REVERT: C 613 MET cc_start: 0.7020 (mpp) cc_final: 0.6467 (mpp) REVERT: D 613 MET cc_start: 0.7334 (mmm) cc_final: 0.7118 (mmm) outliers start: 23 outliers final: 20 residues processed: 97 average time/residue: 0.0579 time to fit residues: 8.1728 Evaluate side-chains 98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 597 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 50.0000 chunk 68 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4051 r_free = 0.4051 target = 0.079703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.058127 restraints weight = 30996.934| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.61 r_work: 0.3298 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8015 Z= 0.154 Angle : 0.728 8.554 11375 Z= 0.403 Chirality : 0.048 0.329 1226 Planarity : 0.006 0.061 1071 Dihedral : 29.573 163.099 2057 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.35 % Favored : 92.35 % Rotamer: Outliers : 3.85 % Allowed : 20.92 % Favored : 75.23 % 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: -0.14 (0.33), residues: 667 helix: 2.10 (0.35), residues: 214 sheet: -1.14 (0.53), residues: 80 loop : -1.22 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 496 TYR 0.010 0.001 TYR A 518 PHE 0.032 0.002 PHE C 610 TRP 0.020 0.001 TRP D 609 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 ( 8015) covalent geometry : angle 0.72827 / 0.40 (11375) hydrogen bonds : bond 0.06906 / 4.77 ( 362) hydrogen bonds : angle 4.67075 / 3.28 ( 1014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 538 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6736 (mtm-85) REVERT: C 605 ASP cc_start: 0.8506 (t0) cc_final: 0.7882 (m-30) REVERT: C 609 TRP cc_start: 0.7915 (t60) cc_final: 0.7484 (t60) REVERT: C 613 MET cc_start: 0.7030 (mpp) cc_final: 0.6368 (mpp) outliers start: 21 outliers final: 20 residues processed: 95 average time/residue: 0.0659 time to fit residues: 9.1940 Evaluate side-chains 99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 610 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 67 optimal weight: 10.0000 chunk 36 optimal weight: 0.0000 chunk 59 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4041 r_free = 0.4041 target = 0.079118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.057522 restraints weight = 31336.794| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.64 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.7578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8015 Z= 0.156 Angle : 0.731 8.730 11375 Z= 0.404 Chirality : 0.047 0.326 1226 Planarity : 0.006 0.064 1071 Dihedral : 29.594 163.503 2057 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.20 % Favored : 92.50 % Rotamer: Outliers : 3.85 % Allowed : 21.47 % Favored : 74.68 % 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: -0.15 (0.33), residues: 667 helix: 2.00 (0.35), residues: 215 sheet: -0.94 (0.53), residues: 78 loop : -1.23 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 594 TYR 0.011 0.001 TYR A 518 PHE 0.018 0.002 PHE A 562 TRP 0.021 0.001 TRP D 609 HIS 0.006 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 ( 8015) covalent geometry : angle 0.73106 / 0.40 (11375) hydrogen bonds : bond 0.06871 / 4.74 ( 362) hydrogen bonds : angle 4.64282 / 3.26 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1846.13 seconds wall clock time: 32 minutes 17.86 seconds (1937.86 seconds total)