Starting phenix.real_space_refine on Fri Sep 11 04:00:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u1t_26305/09_2026/7u1t_26305_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u1t_26305/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u1t_26305/09_2026/7u1t_26305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u1t_26305/09_2026/7u1t_26305.map" model { file = "/net/cci-nas-00/data/ceres_data/7u1t_26305/09_2026/7u1t_26305_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u1t_26305/09_2026/7u1t_26305_neut.cif" } 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-2.2.1-6174/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: 1.87, per 1000 atoms: 0.25 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: 0.75 Conformation dependent library (CDL) restraints added in 338.2 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: 1.13 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: 1.36 Time building geometry restraints manager: 0.98 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 1.20e-02 6.94e+03 3.25e+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: 9220 1.98 - 3.95: 1819 3.95 - 5.93: 251 5.93 - 7.90: 83 7.90 - 9.88: 2 Bond angle restraints: 11375 Sorted by residual: angle pdb=" C3' DT E 10 " pdb=" O3' DT E 10 " pdb=" P DT E 11 " ideal model delta sigma weight residual 119.70 113.90 5.80 1.20e+00 6.94e-01 2.34e+01 angle pdb=" C3' DT F 20 " pdb=" O3' DT F 20 " pdb=" P DA F 21 " ideal model delta sigma weight residual 119.70 113.93 5.77 1.20e+00 6.94e-01 2.31e+01 angle pdb=" C3' DC F 6 " pdb=" O3' DC F 6 " pdb=" P DT F 7 " ideal model delta sigma weight residual 119.70 113.95 5.75 1.20e+00 6.94e-01 2.30e+01 angle pdb=" C3' DC F 4 " pdb=" O3' DC F 4 " pdb=" P DC F 5 " ideal model delta sigma weight residual 119.70 113.96 5.74 1.20e+00 6.94e-01 2.29e+01 angle pdb=" C3' DC F 27 " pdb=" O3' DC F 27 " pdb=" P DC F 28 " ideal model delta sigma weight residual 119.70 113.98 5.72 1.20e+00 6.94e-01 2.27e+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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- 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= 0.947 Angle : 1.601 9.877 11375 Z= 1.118 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 / 0.95 ( 8015) covalent geometry : angle 1.60148 / 1.12 (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 : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 5 residues processed: 201 average time/residue: 0.1040 time to fit residues: 27.1951 Evaluate side-chains 97 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** C 480 ASN D 475 ASN D 480 ASN D 519 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.092976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.071989 restraints weight = 31646.497| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.79 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8015 Z= 0.234 Angle : 0.906 9.736 11375 Z= 0.505 Chirality : 0.058 0.315 1226 Planarity : 0.007 0.048 1071 Dihedral : 29.536 156.745 2061 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.75 % Allowed : 5.10 % Favored : 94.15 % Rotamer: Outliers : 5.69 % Allowed : 15.60 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.31), residues: 667 helix: 2.24 (0.33), residues: 212 sheet: -2.70 (0.43), residues: 94 loop : -1.51 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 538 TYR 0.022 0.003 TYR B 561 PHE 0.023 0.003 PHE A 562 TRP 0.025 0.003 TRP B 464 HIS 0.004 0.001 HIS B 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.23 ( 8015) covalent geometry : angle 0.90621 / 0.50 (11375) hydrogen bonds : bond 0.10407 / 6.87 ( 362) hydrogen bonds : angle 6.67800 / 4.72 ( 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 129 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 467 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7678 (mmmt) REVERT: C 605 ASP cc_start: 0.8106 (t0) cc_final: 0.7241 (m-30) outliers start: 31 outliers final: 20 residues processed: 119 average time/residue: 0.0808 time to fit residues: 13.5692 Evaluate side-chains 105 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 0.0970 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.088386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.066617 restraints weight = 31534.157| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.82 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8015 Z= 0.206 Angle : 0.808 8.313 11375 Z= 0.454 Chirality : 0.051 0.327 1226 Planarity : 0.006 0.038 1071 Dihedral : 29.369 160.429 2061 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.45 % Favored : 93.25 % Rotamer: Outliers : 5.14 % Allowed : 17.61 % 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: -0.64 (0.32), residues: 667 helix: 2.15 (0.34), residues: 212 sheet: -2.82 (0.42), residues: 91 loop : -1.38 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 555 TYR 0.013 0.002 TYR A 561 PHE 0.021 0.003 PHE A 562 TRP 0.019 0.002 TRP A 464 HIS 0.003 0.001 HIS D 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 ( 8015) covalent geometry : angle 0.80763 / 0.45 (11375) hydrogen bonds : bond 0.08438 / 5.62 ( 362) hydrogen bonds : angle 5.79967 / 4.09 ( 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 118 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 TYR cc_start: 0.7976 (p90) cc_final: 0.7688 (p90) REVERT: B 508 PHE cc_start: 0.7680 (t80) cc_final: 0.7263 (t80) REVERT: B 580 LYS cc_start: 0.7079 (mmtm) cc_final: 0.6498 (ttmm) REVERT: C 467 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7802 (mmtt) REVERT: C 563 MET cc_start: 0.8192 (ttp) cc_final: 0.7931 (ttm) REVERT: C 605 ASP cc_start: 0.8120 (t0) cc_final: 0.7325 (m-30) REVERT: C 613 MET cc_start: 0.6832 (mpp) cc_final: 0.6002 (mpp) REVERT: D 563 MET cc_start: 0.7921 (ttm) cc_final: 0.7699 (ttt) REVERT: D 590 THR cc_start: 0.6315 (OUTLIER) cc_final: 0.6062 (p) outliers start: 28 outliers final: 18 residues processed: 109 average time/residue: 0.0712 time to fit residues: 11.4274 Evaluate side-chains 94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 LEU 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 575 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 590 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: 6.9990 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 71 optimal weight: 50.0000 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 0.0040 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.085849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.063710 restraints weight = 31300.475| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.78 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8015 Z= 0.181 Angle : 0.766 8.642 11375 Z= 0.427 Chirality : 0.051 0.355 1226 Planarity : 0.006 0.058 1071 Dihedral : 29.167 156.883 2060 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.60 % Favored : 93.10 % Rotamer: Outliers : 5.69 % Allowed : 18.17 % 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: -0.51 (0.32), residues: 667 helix: 1.93 (0.34), residues: 212 sheet: -2.28 (0.47), residues: 82 loop : -1.26 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 458 TYR 0.012 0.002 TYR B 561 PHE 0.021 0.002 PHE A 562 TRP 0.015 0.002 TRP C 609 HIS 0.002 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 ( 8015) covalent geometry : angle 0.76633 / 0.43 (11375) hydrogen bonds : bond 0.07630 / 5.20 ( 362) hydrogen bonds : angle 5.32223 / 3.75 ( 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 114 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 LYS cc_start: 0.7224 (mmtm) cc_final: 0.6691 (ttmm) REVERT: C 605 ASP cc_start: 0.8152 (t0) cc_final: 0.7407 (m-30) REVERT: C 609 TRP cc_start: 0.7095 (t60) cc_final: 0.6264 (t60) REVERT: C 613 MET cc_start: 0.6736 (mpp) cc_final: 0.5912 (mpp) REVERT: D 563 MET cc_start: 0.7873 (ttm) cc_final: 0.7603 (ttt) outliers start: 31 outliers final: 24 residues processed: 104 average time/residue: 0.0673 time to fit residues: 10.5470 Evaluate side-chains 99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 584 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 609 TRP 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 460 LYS Chi-restraints excluded: chain C residue 494 VAL 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 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: 0.2980 chunk 69 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 3 optimal weight: 0.0570 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.084781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.062760 restraints weight = 30739.762| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.73 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5805 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= 0.162 Angle : 0.734 8.105 11375 Z= 0.412 Chirality : 0.049 0.327 1226 Planarity : 0.006 0.060 1071 Dihedral : 29.148 151.725 2057 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.90 % Favored : 92.80 % Rotamer: Outliers : 5.32 % Allowed : 17.43 % 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: -0.35 (0.33), residues: 667 helix: 2.12 (0.34), residues: 212 sheet: -2.10 (0.51), residues: 83 loop : -1.23 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.015 0.002 TYR B 561 PHE 0.028 0.002 PHE D 562 TRP 0.012 0.001 TRP D 609 HIS 0.002 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 ( 8015) covalent geometry : angle 0.73427 / 0.41 (11375) hydrogen bonds : bond 0.07300 / 5.00 ( 362) hydrogen bonds : angle 5.02150 / 3.55 ( 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 109 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 563 MET cc_start: 0.7852 (tpp) cc_final: 0.7501 (tpp) REVERT: B 580 LYS cc_start: 0.7225 (mmtm) cc_final: 0.6952 (ttmm) REVERT: B 595 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8524 (m) REVERT: C 605 ASP cc_start: 0.8163 (t0) cc_final: 0.7453 (m-30) REVERT: C 609 TRP cc_start: 0.7296 (t60) cc_final: 0.6677 (t60) REVERT: D 613 MET cc_start: 0.7576 (mmm) cc_final: 0.6538 (mpp) outliers start: 29 outliers final: 23 residues processed: 99 average time/residue: 0.0603 time to fit residues: 9.0509 Evaluate side-chains 94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 VAL 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 B residue 475 ASN 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 590 THR Chi-restraints excluded: chain B residue 595 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 541 PHE Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 606 LEU 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: 0.6980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 0.0050 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.084431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.062689 restraints weight = 30765.557| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.67 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8015 Z= 0.154 Angle : 0.728 8.828 11375 Z= 0.405 Chirality : 0.048 0.342 1226 Planarity : 0.006 0.066 1071 Dihedral : 29.163 153.014 2057 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.90 % Favored : 92.80 % Rotamer: Outliers : 4.04 % Allowed : 18.90 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.33), residues: 667 helix: 2.30 (0.35), residues: 212 sheet: -1.82 (0.52), residues: 83 loop : -1.17 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 594 TYR 0.016 0.002 TYR B 561 PHE 0.030 0.002 PHE D 562 TRP 0.012 0.001 TRP D 609 HIS 0.003 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 8015) covalent geometry : angle 0.72778 / 0.40 (11375) hydrogen bonds : bond 0.07125 / 4.87 ( 362) hydrogen bonds : angle 4.79356 / 3.36 ( 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 100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 563 MET cc_start: 0.7882 (tpp) cc_final: 0.7512 (tpp) REVERT: B 580 LYS cc_start: 0.7273 (mmtm) cc_final: 0.6766 (ttmm) REVERT: C 605 ASP cc_start: 0.8211 (t0) cc_final: 0.7509 (m-30) REVERT: C 609 TRP cc_start: 0.7320 (t60) cc_final: 0.6712 (t60) REVERT: C 613 MET cc_start: 0.6866 (mpp) cc_final: 0.6379 (mpp) outliers start: 22 outliers final: 19 residues processed: 96 average time/residue: 0.0633 time to fit residues: 9.1554 Evaluate side-chains 93 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 590 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 596 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 526 LEU 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: 20.0000 chunk 57 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.080247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.058213 restraints weight = 30980.450| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.74 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 8015 Z= 0.187 Angle : 0.770 8.914 11375 Z= 0.424 Chirality : 0.049 0.356 1226 Planarity : 0.006 0.059 1071 Dihedral : 29.370 162.743 2057 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.90 % Favored : 92.80 % Rotamer: Outliers : 4.40 % Allowed : 19.08 % 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: -0.28 (0.32), residues: 667 helix: 2.19 (0.35), residues: 206 sheet: -1.64 (0.51), residues: 83 loop : -1.25 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 469 TYR 0.015 0.002 TYR A 518 PHE 0.025 0.002 PHE D 562 TRP 0.017 0.002 TRP D 609 HIS 0.003 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 ( 8015) covalent geometry : angle 0.77033 / 0.42 (11375) hydrogen bonds : bond 0.07564 / 5.22 ( 362) hydrogen bonds : angle 4.77066 / 3.34 ( 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 109 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 563 MET cc_start: 0.8010 (tpp) cc_final: 0.7680 (tpp) REVERT: B 538 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6414 (mtm-85) REVERT: C 605 ASP cc_start: 0.8299 (t0) cc_final: 0.7692 (m-30) REVERT: C 609 TRP cc_start: 0.7668 (t60) cc_final: 0.6925 (t60) REVERT: C 613 MET cc_start: 0.6949 (mpp) cc_final: 0.6261 (mpp) outliers start: 24 outliers final: 19 residues processed: 104 average time/residue: 0.0692 time to fit residues: 10.3783 Evaluate side-chains 101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 590 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 596 THR 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 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: 1.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.079137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.057050 restraints weight = 31159.011| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.72 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8015 Z= 0.171 Angle : 0.750 7.682 11375 Z= 0.415 Chirality : 0.049 0.359 1226 Planarity : 0.006 0.062 1071 Dihedral : 29.475 173.393 2057 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.90 % Favored : 92.95 % Rotamer: Outliers : 4.40 % Allowed : 19.63 % Favored : 75.96 % 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: -0.24 (0.33), residues: 667 helix: 2.19 (0.35), residues: 206 sheet: -1.56 (0.50), residues: 84 loop : -1.21 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 522 TYR 0.013 0.002 TYR A 518 PHE 0.021 0.002 PHE A 562 TRP 0.017 0.002 TRP D 609 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 ( 8015) covalent geometry : angle 0.75002 / 0.41 (11375) hydrogen bonds : bond 0.07167 / 4.93 ( 362) hydrogen bonds : angle 4.68160 / 3.28 ( 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 108 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 563 MET cc_start: 0.8005 (tpp) cc_final: 0.7668 (tpp) REVERT: B 538 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6884 (mtm-85) REVERT: C 605 ASP cc_start: 0.8315 (t0) cc_final: 0.7759 (m-30) REVERT: C 609 TRP cc_start: 0.7668 (t60) cc_final: 0.6901 (t60) REVERT: C 613 MET cc_start: 0.6985 (mpp) cc_final: 0.6335 (mpp) REVERT: D 500 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8126 (mp0) outliers start: 24 outliers final: 17 residues processed: 102 average time/residue: 0.0653 time to fit residues: 9.7337 Evaluate side-chains 99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 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 494 VAL 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 475 ASN Chi-restraints excluded: chain D residue 494 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.079843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.057900 restraints weight = 31016.688| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.71 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.7040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8015 Z= 0.154 Angle : 0.750 9.499 11375 Z= 0.413 Chirality : 0.050 0.360 1226 Planarity : 0.006 0.063 1071 Dihedral : 29.490 170.060 2057 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.50 % Favored : 92.35 % Rotamer: Outliers : 3.67 % Allowed : 19.82 % 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: -0.08 (0.33), residues: 667 helix: 2.28 (0.35), residues: 208 sheet: -1.25 (0.52), residues: 78 loop : -1.18 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 522 TYR 0.013 0.001 TYR B 561 PHE 0.022 0.002 PHE D 562 TRP 0.023 0.002 TRP D 609 HIS 0.009 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 ( 8015) covalent geometry : angle 0.74970 / 0.41 (11375) hydrogen bonds : bond 0.06899 / 4.75 ( 362) hydrogen bonds : angle 4.64376 / 3.29 ( 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 100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 563 MET cc_start: 0.7949 (tpp) cc_final: 0.7613 (tpp) REVERT: C 605 ASP cc_start: 0.8229 (t0) cc_final: 0.7609 (m-30) REVERT: C 609 TRP cc_start: 0.7596 (t60) cc_final: 0.6826 (t60) REVERT: C 613 MET cc_start: 0.6993 (mpp) cc_final: 0.6315 (mpp) REVERT: D 500 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8048 (mp0) outliers start: 20 outliers final: 19 residues processed: 95 average time/residue: 0.0700 time to fit residues: 9.8343 Evaluate side-chains 98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 538 ARG Chi-restraints excluded: chain B residue 583 VAL 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 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 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 71 optimal weight: 50.0000 chunk 68 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.078941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.057088 restraints weight = 31409.773| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.72 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.7176 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= 0.164 Angle : 0.749 8.721 11375 Z= 0.413 Chirality : 0.049 0.363 1226 Planarity : 0.007 0.063 1071 Dihedral : 29.503 166.752 2057 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.35 % Favored : 92.50 % Rotamer: Outliers : 3.67 % Allowed : 20.55 % Favored : 75.78 % 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: -0.10 (0.33), residues: 667 helix: 2.20 (0.35), residues: 208 sheet: -1.19 (0.52), residues: 79 loop : -1.17 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 491 TYR 0.013 0.002 TYR A 518 PHE 0.020 0.002 PHE D 562 TRP 0.021 0.002 TRP D 609 HIS 0.026 0.002 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 8015) covalent geometry : angle 0.74934 / 0.41 (11375) hydrogen bonds : bond 0.07016 / 4.84 ( 362) hydrogen bonds : angle 4.63319 / 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 98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 563 MET cc_start: 0.7992 (tpp) cc_final: 0.7658 (tpp) REVERT: C 605 ASP cc_start: 0.8310 (t0) cc_final: 0.7728 (m-30) REVERT: C 609 TRP cc_start: 0.7777 (t60) cc_final: 0.7075 (t60) REVERT: D 500 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8171 (mp0) outliers start: 20 outliers final: 18 residues processed: 95 average time/residue: 0.0699 time to fit residues: 9.8221 Evaluate side-chains 94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 507 VAL Chi-restraints excluded: chain B residue 526 LEU 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 494 VAL 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 475 ASN 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: 0.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 36 optimal weight: 0.1980 chunk 59 optimal weight: 0.0970 chunk 73 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.078932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.057025 restraints weight = 31342.092| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.71 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 8015 Z= 0.262 Angle : 1.040 59.200 11375 Z= 0.616 Chirality : 0.059 1.164 1226 Planarity : 0.007 0.064 1071 Dihedral : 29.504 166.736 2057 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.50 % Favored : 92.35 % Rotamer: Outliers : 3.30 % Allowed : 20.55 % Favored : 76.15 % Cbeta Deviations : 0.17 % 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: -0.09 (0.33), residues: 667 helix: 2.20 (0.35), residues: 208 sheet: -1.19 (0.52), residues: 79 loop : -1.15 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 491 TYR 0.012 0.001 TYR A 518 PHE 0.020 0.002 PHE D 562 TRP 0.018 0.002 TRP D 609 HIS 0.019 0.002 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.26 ( 8015) covalent geometry : angle 1.03993 / 0.62 (11375) hydrogen bonds : bond 0.07031 / 4.86 ( 362) hydrogen bonds : angle 4.63557 / 3.28 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1991.42 seconds wall clock time: 34 minutes 48.60 seconds (2088.60 seconds total)