Starting phenix.real_space_refine on Wed Feb 12 06:53:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u1t_26305/02_2025/7u1t_26305_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u1t_26305/02_2025/7u1t_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_26305/02_2025/7u1t_26305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u1t_26305/02_2025/7u1t_26305.map" model { file = "/net/cci-nas-00/data/ceres_data/7u1t_26305/02_2025/7u1t_26305_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u1t_26305/02_2025/7u1t_26305_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.26, per 1000 atoms: 0.69 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: 1.91 Conformation dependent library (CDL) restraints added in 764.6 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: 3.67 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: 2.67 Time building geometry restraints manager: 2.23 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=" 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=" N VAL D 509 " pdb=" CA VAL D 509 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N VAL B 595 " pdb=" CA VAL B 595 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.06e+01 ... (remaining 8010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 9076 1.92 - 3.83: 1928 3.83 - 5.75: 238 5.75 - 7.66: 128 7.66 - 9.58: 5 Bond angle restraints: 11375 Sorted by residual: angle pdb=" C4' DG F 56 " pdb=" C3' DG F 56 " pdb=" O3' DG F 56 " ideal model delta sigma weight residual 110.00 119.58 -9.58 1.50e+00 4.44e-01 4.08e+01 angle pdb=" O3' DC F 49 " pdb=" C3' DC F 49 " pdb=" C2' DC F 49 " ideal model delta sigma weight residual 111.50 102.42 9.08 1.50e+00 4.44e-01 3.66e+01 angle pdb=" C4' DT F 54 " pdb=" C3' DT F 54 " pdb=" O3' DT F 54 " ideal model delta sigma weight residual 110.00 118.69 -8.69 1.50e+00 4.44e-01 3.36e+01 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=" 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 ... (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 - 0.125: 946 0.125 - 0.251: 165 0.251 - 0.376: 6 0.376 - 0.501: 81 0.501 - 0.626: 28 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 2.35 2.97 -0.63 2.00e-01 2.50e+01 9.80e+00 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 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.34e+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 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.09e+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: 0.010 Normalize map: mean=0, sd=1: 1.140 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.510 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5202 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= 0.790 Angle : 1.628 9.577 11375 Z= 1.085 Chirality : 0.168 0.626 1226 Planarity : 0.002 0.010 1071 Dihedral : 24.341 179.086 3302 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 57.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP D 503 HIS 0.003 0.001 HIS A 569 PHE 0.008 0.001 PHE D 571 TYR 0.004 0.001 TYR D 510 ARG 0.003 0.001 ARG A 486 *********************** 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 : 0.683 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: 0.2457 time to fit residues: 62.4460 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 : 0.685 ------------------------------------------------------------------------------- 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 64 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN B 475 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4151 r_free = 0.4151 target = 0.085816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.064159 restraints weight = 31089.183| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.81 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8015 Z= 0.327 Angle : 0.867 9.428 11375 Z= 0.471 Chirality : 0.048 0.226 1226 Planarity : 0.006 0.036 1071 Dihedral : 29.175 172.032 2061 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.25 % Favored : 94.15 % Rotamer: Outliers : 6.42 % Allowed : 15.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.32), residues: 667 helix: 2.45 (0.33), residues: 212 sheet: -2.36 (0.49), residues: 78 loop : -1.50 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 464 HIS 0.007 0.002 HIS B 569 PHE 0.013 0.002 PHE A 562 TYR 0.020 0.003 TYR B 510 ARG 0.006 0.001 ARG B 594 *********************** 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 128 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8114 (m-30) cc_final: 0.7899 (m-30) REVERT: B 475 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.6865 (m-40) REVERT: B 580 LYS cc_start: 0.7308 (mmtm) cc_final: 0.6710 (ttmm) REVERT: C 605 ASP cc_start: 0.8191 (t0) cc_final: 0.7494 (m-30) REVERT: C 613 MET cc_start: 0.6672 (mpp) cc_final: 0.5889 (mpp) REVERT: D 584 MET cc_start: 0.8869 (tmm) cc_final: 0.8658 (tmm) REVERT: D 609 TRP cc_start: 0.5262 (t-100) cc_final: 0.5024 (t-100) outliers start: 35 outliers final: 17 residues processed: 119 average time/residue: 0.1892 time to fit residues: 30.6610 Evaluate side-chains 92 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain B residue 475 ASN 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 557 SER 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 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 25 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 GLN C 480 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.080351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.058498 restraints weight = 31426.618| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.68 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8015 Z= 0.280 Angle : 0.758 8.444 11375 Z= 0.419 Chirality : 0.042 0.162 1226 Planarity : 0.006 0.073 1071 Dihedral : 28.973 155.199 2060 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.45 % Favored : 93.25 % Rotamer: Outliers : 5.32 % Allowed : 17.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.32), residues: 667 helix: 2.29 (0.33), residues: 206 sheet: -2.18 (0.48), residues: 79 loop : -1.48 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 464 HIS 0.002 0.001 HIS C 493 PHE 0.019 0.002 PHE A 562 TYR 0.016 0.002 TYR A 518 ARG 0.006 0.001 ARG D 469 *********************** 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 114 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8232 (m-30) cc_final: 0.7978 (m-30) REVERT: C 605 ASP cc_start: 0.8308 (t0) cc_final: 0.7778 (m-30) REVERT: D 609 TRP cc_start: 0.5575 (t-100) cc_final: 0.5135 (t-100) outliers start: 29 outliers final: 19 residues processed: 107 average time/residue: 0.1626 time to fit residues: 24.8486 Evaluate side-chains 92 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain A residue 562 PHE 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 543 MET Chi-restraints excluded: chain B residue 574 VAL 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 575 LEU Chi-restraints excluded: chain C residue 597 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 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 38 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3948 r_free = 0.3948 target = 0.075129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.053448 restraints weight = 31494.932| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.58 r_work: 0.3164 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.7681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8015 Z= 0.331 Angle : 0.763 8.182 11375 Z= 0.425 Chirality : 0.043 0.159 1226 Planarity : 0.007 0.073 1071 Dihedral : 29.499 171.181 2057 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.20 % Favored : 92.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.32), residues: 667 helix: 2.01 (0.34), residues: 206 sheet: -1.62 (0.50), residues: 75 loop : -1.53 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 503 HIS 0.003 0.001 HIS D 569 PHE 0.021 0.002 PHE A 562 TYR 0.022 0.002 TYR A 518 ARG 0.009 0.001 ARG B 496 *********************** 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: 23 poor density : 82 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8400 (m-30) cc_final: 0.8110 (m-30) REVERT: C 605 ASP cc_start: 0.8645 (t0) cc_final: 0.8055 (m-30) REVERT: D 609 TRP cc_start: 0.5843 (t-100) cc_final: 0.5274 (t-100) outliers start: 23 outliers final: 20 residues processed: 97 average time/residue: 0.1668 time to fit residues: 23.0931 Evaluate side-chains 90 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 562 PHE 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 543 MET Chi-restraints excluded: chain B residue 574 VAL 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 595 VAL Chi-restraints excluded: chain C residue 597 VAL 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 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 2 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3933 r_free = 0.3933 target = 0.075106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.053780 restraints weight = 31273.668| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.57 r_work: 0.3149 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.8319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8015 Z= 0.286 Angle : 0.736 8.360 11375 Z= 0.405 Chirality : 0.042 0.173 1226 Planarity : 0.007 0.067 1071 Dihedral : 29.433 167.838 2057 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.65 % Favored : 92.05 % Rotamer: Outliers : 4.59 % Allowed : 18.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.32), residues: 667 helix: 1.95 (0.34), residues: 208 sheet: -1.27 (0.49), residues: 80 loop : -1.49 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 464 HIS 0.003 0.001 HIS D 493 PHE 0.030 0.002 PHE C 610 TYR 0.017 0.002 TYR A 518 ARG 0.019 0.001 ARG D 459 *********************** 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 99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8366 (m-30) cc_final: 0.8041 (m-30) REVERT: C 500 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7380 (mp0) REVERT: C 605 ASP cc_start: 0.8661 (t0) cc_final: 0.8123 (m-30) REVERT: C 613 MET cc_start: 0.7267 (mpp) cc_final: 0.5792 (mmt) REVERT: D 495 GLU cc_start: 0.7858 (tt0) cc_final: 0.7488 (pm20) REVERT: D 609 TRP cc_start: 0.5973 (t-100) cc_final: 0.5336 (t-100) outliers start: 25 outliers final: 20 residues processed: 91 average time/residue: 0.1570 time to fit residues: 20.9725 Evaluate side-chains 91 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain A residue 562 PHE 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 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 595 VAL Chi-restraints excluded: chain C residue 597 VAL 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 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 38 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 33 optimal weight: 0.0970 overall best weight: 2.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 GLN D 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.072664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.051225 restraints weight = 32209.178| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.60 r_work: 0.3091 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.8926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8015 Z= 0.322 Angle : 0.752 7.055 11375 Z= 0.414 Chirality : 0.043 0.164 1226 Planarity : 0.007 0.072 1071 Dihedral : 29.596 165.714 2055 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.50 % Favored : 92.20 % Rotamer: Outliers : 4.77 % Allowed : 18.35 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.31), residues: 667 helix: 1.74 (0.33), residues: 209 sheet: -0.88 (0.52), residues: 71 loop : -1.67 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 503 HIS 0.003 0.001 HIS A 493 PHE 0.021 0.002 PHE A 562 TYR 0.016 0.002 TYR A 518 ARG 0.005 0.001 ARG D 459 *********************** 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 101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8379 (m-30) cc_final: 0.8025 (m-30) REVERT: B 543 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6515 (pmm) REVERT: C 495 GLU cc_start: 0.7736 (mp0) cc_final: 0.7526 (mp0) REVERT: C 500 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7648 (mp0) REVERT: C 605 ASP cc_start: 0.8699 (t0) cc_final: 0.8150 (m-30) REVERT: C 613 MET cc_start: 0.7407 (mpp) cc_final: 0.5859 (mmt) REVERT: D 488 LEU cc_start: 0.8909 (mm) cc_final: 0.8684 (mm) REVERT: D 609 TRP cc_start: 0.6052 (t-100) cc_final: 0.5344 (t-100) outliers start: 26 outliers final: 22 residues processed: 92 average time/residue: 0.1779 time to fit residues: 23.6890 Evaluate side-chains 91 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 569 HIS 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 543 MET Chi-restraints excluded: chain B residue 574 VAL 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 493 HIS Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 597 VAL 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 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 13 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 480 ASN ** 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 = 0.3934 r_free = 0.3934 target = 0.074138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.052857 restraints weight = 31640.896| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.62 r_work: 0.3150 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.9054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8015 Z= 0.237 Angle : 0.712 9.380 11375 Z= 0.391 Chirality : 0.041 0.173 1226 Planarity : 0.007 0.067 1071 Dihedral : 29.438 171.442 2055 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.20 % Favored : 92.50 % Rotamer: Outliers : 4.40 % Allowed : 19.27 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.32), residues: 667 helix: 2.01 (0.34), residues: 209 sheet: -1.10 (0.49), residues: 80 loop : -1.53 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 464 HIS 0.002 0.001 HIS A 468 PHE 0.040 0.002 PHE C 610 TYR 0.011 0.002 TYR A 518 ARG 0.006 0.000 ARG D 459 *********************** 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: 24 poor density : 79 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8399 (m-30) cc_final: 0.8055 (m-30) REVERT: B 538 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6892 (mtm-85) REVERT: B 543 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6553 (pmm) REVERT: C 500 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7784 (mp0) REVERT: C 605 ASP cc_start: 0.8643 (t0) cc_final: 0.8097 (m-30) REVERT: C 613 MET cc_start: 0.7374 (mpp) cc_final: 0.5832 (mmt) REVERT: D 495 GLU cc_start: 0.8440 (tt0) cc_final: 0.7877 (pm20) REVERT: D 598 CYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7201 (p) REVERT: D 609 TRP cc_start: 0.6087 (t-100) cc_final: 0.5348 (t-100) outliers start: 24 outliers final: 20 residues processed: 95 average time/residue: 0.1527 time to fit residues: 21.1457 Evaluate side-chains 94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain A residue 562 PHE 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 543 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL 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 597 VAL Chi-restraints excluded: chain D residue 598 CYS 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: 10.0000 chunk 21 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 480 ASN ** 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 = 0.3900 r_free = 0.3900 target = 0.073382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.051752 restraints weight = 32403.350| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.73 r_work: 0.3096 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.9261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8015 Z= 0.252 Angle : 0.725 8.892 11375 Z= 0.398 Chirality : 0.042 0.225 1226 Planarity : 0.007 0.086 1071 Dihedral : 29.506 171.092 2055 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.95 % Favored : 91.75 % Rotamer: Outliers : 4.95 % Allowed : 19.63 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.32), residues: 667 helix: 1.92 (0.34), residues: 209 sheet: -1.06 (0.50), residues: 80 loop : -1.56 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 464 HIS 0.002 0.001 HIS A 468 PHE 0.019 0.002 PHE A 562 TYR 0.012 0.002 TYR A 518 ARG 0.005 0.000 ARG D 459 *********************** 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: 27 poor density : 75 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8411 (m-30) cc_final: 0.8060 (m-30) REVERT: B 538 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6892 (mtm-85) REVERT: B 543 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6574 (pmm) REVERT: C 500 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7812 (mp0) REVERT: C 605 ASP cc_start: 0.8671 (t0) cc_final: 0.8105 (m-30) REVERT: C 613 MET cc_start: 0.7433 (mpp) cc_final: 0.5955 (mmt) REVERT: D 598 CYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7121 (p) REVERT: D 609 TRP cc_start: 0.6121 (t-100) cc_final: 0.5383 (t-100) outliers start: 27 outliers final: 20 residues processed: 94 average time/residue: 0.1531 time to fit residues: 20.9696 Evaluate side-chains 94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain A residue 562 PHE 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 543 MET 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 493 HIS Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 598 CYS 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 64 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 480 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.074477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.052878 restraints weight = 32554.874| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.77 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.9387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8015 Z= 0.222 Angle : 0.729 8.772 11375 Z= 0.398 Chirality : 0.041 0.210 1226 Planarity : 0.007 0.082 1071 Dihedral : 29.434 172.856 2055 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.90 % Favored : 92.80 % Rotamer: Outliers : 4.40 % Allowed : 20.73 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.32), residues: 667 helix: 1.97 (0.34), residues: 208 sheet: -1.18 (0.50), residues: 83 loop : -1.50 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.004 0.001 HIS D 493 PHE 0.017 0.001 PHE A 562 TYR 0.010 0.002 TYR A 518 ARG 0.005 0.000 ARG D 459 *********************** 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 101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8238 (m-30) cc_final: 0.7895 (m-30) REVERT: B 538 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6851 (mtm-85) REVERT: B 543 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6698 (pmm) REVERT: C 500 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7749 (mp0) REVERT: C 605 ASP cc_start: 0.8372 (t0) cc_final: 0.7931 (m-30) REVERT: C 613 MET cc_start: 0.7306 (mpp) cc_final: 0.5858 (mmt) REVERT: D 598 CYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7012 (p) REVERT: D 609 TRP cc_start: 0.6020 (t-100) cc_final: 0.5263 (t-100) outliers start: 24 outliers final: 20 residues processed: 91 average time/residue: 0.1583 time to fit residues: 20.8745 Evaluate side-chains 96 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 562 PHE Chi-restraints excluded: chain A residue 576 LYS 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 543 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 598 CYS 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 42 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 480 ASN ** 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 = 0.3908 r_free = 0.3908 target = 0.073599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.052002 restraints weight = 32506.654| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.73 r_work: 0.3107 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.9580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8015 Z= 0.247 Angle : 0.738 8.928 11375 Z= 0.403 Chirality : 0.041 0.210 1226 Planarity : 0.007 0.076 1071 Dihedral : 29.480 173.026 2055 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.95 % Favored : 91.75 % Rotamer: Outliers : 4.95 % Allowed : 20.00 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.32), residues: 667 helix: 2.02 (0.34), residues: 207 sheet: -0.96 (0.51), residues: 80 loop : -1.53 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 464 HIS 0.002 0.001 HIS A 468 PHE 0.019 0.002 PHE A 562 TYR 0.011 0.002 TYR A 518 ARG 0.004 0.000 ARG D 459 ********************** 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: 27 poor density : 73 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8384 (m-30) cc_final: 0.8046 (m-30) REVERT: B 483 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8824 (pp20) REVERT: B 538 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6801 (mtm-85) REVERT: B 543 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6652 (pmm) REVERT: C 500 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7792 (mp0) REVERT: C 605 ASP cc_start: 0.8643 (t0) cc_final: 0.8086 (m-30) REVERT: C 613 MET cc_start: 0.7381 (mpp) cc_final: 0.5876 (mmt) REVERT: D 598 CYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6930 (p) REVERT: D 609 TRP cc_start: 0.6264 (t-100) cc_final: 0.5644 (t-100) outliers start: 27 outliers final: 23 residues processed: 90 average time/residue: 0.1504 time to fit residues: 19.7950 Evaluate side-chains 96 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 LYS 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 543 MET Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 465 PHE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 598 CYS 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 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.076286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.055017 restraints weight = 32019.679| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.78 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.9691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8015 Z= 0.202 Angle : 0.713 9.207 11375 Z= 0.389 Chirality : 0.041 0.216 1226 Planarity : 0.007 0.072 1071 Dihedral : 29.348 174.241 2055 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.85 % Favored : 93.85 % Rotamer: Outliers : 3.67 % Allowed : 21.28 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.32), residues: 667 helix: 2.18 (0.35), residues: 209 sheet: -1.13 (0.50), residues: 83 loop : -1.49 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 464 HIS 0.002 0.000 HIS A 468 PHE 0.017 0.001 PHE C 508 TYR 0.009 0.002 TYR B 510 ARG 0.004 0.000 ARG D 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4484.19 seconds wall clock time: 80 minutes 0.84 seconds (4800.84 seconds total)