Starting phenix.real_space_refine on Wed Mar 12 06:55:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u1t_26305/03_2025/7u1t_26305_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u1t_26305/03_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_26305/03_2025/7u1t_26305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u1t_26305/03_2025/7u1t_26305.map" model { file = "/net/cci-nas-00/data/ceres_data/7u1t_26305/03_2025/7u1t_26305_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u1t_26305/03_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-5624/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: 5.18, per 1000 atoms: 0.68 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: 2.30 Conformation dependent library (CDL) restraints added in 983.5 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: 3.16 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: 2.34 Time building geometry restraints manager: 2.43 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: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.120 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.680 ------------------------------------------------------------------------------- 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 : 0.611 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: 0.2362 time to fit residues: 60.1971 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 : 0.663 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.064159 restraints weight = 31089.184| |-----------------------------------------------------------------------------| 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 : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8113 (m-30) cc_final: 0.7898 (m-30) REVERT: B 475 ASN cc_start: 0.7361 (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: 0.1796 time to fit residues: 29.3788 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 : 0.671 ------------------------------------------------------------------------------- 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: 0.1980 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN C 480 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.083662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.062086 restraints weight = 31334.705| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.66 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.6111 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= 0.242 Angle : 0.726 8.719 11375 Z= 0.403 Chirality : 0.041 0.162 1226 Planarity : 0.006 0.069 1071 Dihedral : 28.833 160.194 2060 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.30 % Favored : 93.40 % Rotamer: Outliers : 4.95 % Allowed : 17.61 % Favored : 77.43 % 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: -0.27 (0.32), residues: 667 helix: 2.44 (0.34), residues: 212 sheet: -2.05 (0.49), residues: 78 loop : -1.38 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 464 HIS 0.002 0.001 HIS A 468 PHE 0.018 0.002 PHE A 562 TYR 0.013 0.002 TYR B 561 ARG 0.004 0.001 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 573 GLU cc_start: 0.9094 (tt0) cc_final: 0.8887 (tt0) REVERT: A 605 ASP cc_start: 0.8209 (m-30) cc_final: 0.7956 (m-30) REVERT: B 580 LYS cc_start: 0.7395 (mmtm) cc_final: 0.6827 (ttmm) REVERT: C 605 ASP cc_start: 0.8161 (t0) cc_final: 0.7515 (m-30) REVERT: D 584 MET cc_start: 0.8880 (tmm) cc_final: 0.8671 (tmm) REVERT: D 586 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6174 (ttpt) REVERT: D 609 TRP cc_start: 0.5398 (t-100) cc_final: 0.5016 (t-100) outliers start: 27 outliers final: 18 residues processed: 107 average time/residue: 0.1630 time to fit residues: 24.6100 Evaluate side-chains 95 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 568 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL 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 597 VAL Chi-restraints excluded: chain D residue 541 PHE Chi-restraints excluded: chain D residue 586 LYS 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: 4.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 0.0470 chunk 41 optimal weight: 0.6980 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: 3.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.081100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.059328 restraints weight = 31007.206| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.57 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.6920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8015 Z= 0.230 Angle : 0.707 7.926 11375 Z= 0.393 Chirality : 0.040 0.158 1226 Planarity : 0.006 0.067 1071 Dihedral : 29.150 175.413 2058 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.30 % Favored : 93.40 % Rotamer: Outliers : 3.85 % Allowed : 17.80 % Favored : 78.35 % 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: -0.17 (0.32), residues: 667 helix: 2.51 (0.34), residues: 207 sheet: -1.67 (0.49), residues: 81 loop : -1.33 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 464 HIS 0.006 0.001 HIS B 493 PHE 0.024 0.002 PHE D 562 TYR 0.013 0.002 TYR A 518 ARG 0.014 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 109 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8167 (m-30) cc_final: 0.7911 (m-30) REVERT: C 605 ASP cc_start: 0.8281 (t0) cc_final: 0.7729 (m-30) REVERT: D 609 TRP cc_start: 0.5563 (t-100) cc_final: 0.5104 (t-100) REVERT: D 613 MET cc_start: 0.8347 (mpp) cc_final: 0.7838 (mpp) outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 0.1424 time to fit residues: 21.1634 Evaluate side-chains 99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 562 PHE Chi-restraints excluded: chain A residue 568 THR 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 583 VAL Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 504 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.073842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.052086 restraints weight = 32007.071| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.62 r_work: 0.3101 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.8223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8015 Z= 0.335 Angle : 0.774 8.590 11375 Z= 0.429 Chirality : 0.043 0.160 1226 Planarity : 0.007 0.059 1071 Dihedral : 29.458 159.360 2058 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.10 % Favored : 91.60 % Rotamer: Outliers : 5.32 % Allowed : 16.33 % Favored : 78.35 % 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: -0.45 (0.32), residues: 667 helix: 1.92 (0.34), residues: 206 sheet: -1.09 (0.53), residues: 74 loop : -1.46 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 464 HIS 0.004 0.001 HIS B 493 PHE 0.021 0.002 PHE A 562 TYR 0.022 0.002 TYR A 518 ARG 0.005 0.001 ARG D 469 *********************** 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 110 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 577 ASP cc_start: 0.8725 (m-30) cc_final: 0.8524 (m-30) REVERT: A 605 ASP cc_start: 0.8427 (m-30) cc_final: 0.8121 (m-30) REVERT: C 575 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8559 (tt) REVERT: C 605 ASP cc_start: 0.8724 (t0) cc_final: 0.8175 (m-30) REVERT: D 609 TRP cc_start: 0.6051 (t-100) cc_final: 0.5386 (t-100) REVERT: D 613 MET cc_start: 0.8657 (mpp) cc_final: 0.8210 (mpp) outliers start: 29 outliers final: 22 residues processed: 102 average time/residue: 0.1490 time to fit residues: 22.2566 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 : 0.607 ------------------------------------------------------------------------------- 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 516 SER 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 585 THR Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 504 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 33 optimal weight: 0.0170 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 HIS ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.076667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.055301 restraints weight = 31178.728| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.59 r_work: 0.3217 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.8373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8015 Z= 0.212 Angle : 0.710 9.224 11375 Z= 0.391 Chirality : 0.041 0.190 1226 Planarity : 0.006 0.063 1071 Dihedral : 29.318 163.156 2057 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.55 % Favored : 94.15 % Rotamer: Outliers : 3.67 % Allowed : 19.27 % Favored : 77.06 % 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: -0.16 (0.32), residues: 667 helix: 2.34 (0.34), residues: 208 sheet: -1.13 (0.51), residues: 83 loop : -1.35 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.010 0.001 HIS B 493 PHE 0.017 0.002 PHE A 562 TYR 0.011 0.002 TYR A 518 ARG 0.005 0.000 ARG D 496 *********************** 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 96 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8335 (m-30) cc_final: 0.8016 (m-30) REVERT: C 500 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7473 (mp0) REVERT: C 605 ASP cc_start: 0.8644 (t0) cc_final: 0.8083 (m-30) REVERT: D 609 TRP cc_start: 0.6051 (t-100) cc_final: 0.5392 (t-100) REVERT: D 613 MET cc_start: 0.8574 (mpp) cc_final: 0.8078 (mpp) outliers start: 20 outliers final: 16 residues processed: 88 average time/residue: 0.1386 time to fit residues: 18.2689 Evaluate side-chains 86 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 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 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 610 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.073682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.052270 restraints weight = 31673.459| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.60 r_work: 0.3127 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.8761 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= 0.302 Angle : 0.735 8.606 11375 Z= 0.407 Chirality : 0.042 0.169 1226 Planarity : 0.007 0.065 1071 Dihedral : 29.507 165.201 2055 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.40 % Favored : 91.30 % 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: -0.28 (0.32), residues: 667 helix: 2.08 (0.34), residues: 209 sheet: -0.75 (0.52), residues: 74 loop : -1.44 (0.31), residues: 384 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 0.021 0.002 PHE A 562 TYR 0.016 0.002 TYR A 518 ARG 0.004 0.001 ARG C 486 *********************** 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 102 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8414 (m-30) cc_final: 0.8065 (m-30) REVERT: C 500 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7517 (mp0) REVERT: C 605 ASP cc_start: 0.8715 (t0) cc_final: 0.8171 (m-30) REVERT: D 488 LEU cc_start: 0.8813 (mm) cc_final: 0.8594 (mm) REVERT: D 500 GLU cc_start: 0.8433 (mp0) cc_final: 0.7985 (mp0) REVERT: D 609 TRP cc_start: 0.6102 (t-100) cc_final: 0.5372 (t-100) REVERT: D 613 MET cc_start: 0.8572 (mpp) cc_final: 0.8076 (mpp) outliers start: 24 outliers final: 21 residues processed: 93 average time/residue: 0.1481 time to fit residues: 20.6185 Evaluate side-chains 92 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 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 526 LEU 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 516 SER 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 504 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 543 MET 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=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: 4.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.0020 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- 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** D 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.073985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.052694 restraints weight = 32214.346| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.63 r_work: 0.3139 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.9019 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= 0.266 Angle : 0.722 8.906 11375 Z= 0.397 Chirality : 0.042 0.193 1226 Planarity : 0.007 0.094 1071 Dihedral : 29.463 169.157 2055 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.50 % Favored : 92.20 % 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 : 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: -0.28 (0.32), residues: 667 helix: 2.07 (0.34), residues: 208 sheet: -0.73 (0.51), residues: 77 loop : -1.44 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 464 HIS 0.002 0.001 HIS A 468 PHE 0.019 0.002 PHE A 562 TYR 0.014 0.002 TYR A 518 ARG 0.003 0.000 ARG C 486 *********************** 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 101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8409 (m-30) cc_final: 0.8055 (m-30) REVERT: B 543 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6492 (pmm) REVERT: C 500 GLU cc_start: 0.8567 (mm-30) cc_final: 0.7799 (mp0) REVERT: C 605 ASP cc_start: 0.8676 (t0) cc_final: 0.8142 (m-30) REVERT: C 613 MET cc_start: 0.7192 (mpp) cc_final: 0.5626 (mmt) REVERT: D 488 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8503 (mm) REVERT: D 609 TRP cc_start: 0.6095 (t-100) cc_final: 0.5523 (t-100) REVERT: D 613 MET cc_start: 0.8578 (mpp) cc_final: 0.8097 (mpp) outliers start: 24 outliers final: 21 residues processed: 92 average time/residue: 0.1432 time to fit residues: 19.9034 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 : 0.675 ------------------------------------------------------------------------------- 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 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 526 LEU 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 494 VAL Chi-restraints excluded: chain C residue 516 SER 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 488 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 543 MET 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 64 optimal weight: 8.9990 chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.075786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.054509 restraints weight = 32329.653| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.68 r_work: 0.3197 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.9112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8015 Z= 0.211 Angle : 0.714 9.438 11375 Z= 0.392 Chirality : 0.041 0.236 1226 Planarity : 0.007 0.081 1071 Dihedral : 29.409 171.603 2055 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.05 % Favored : 92.65 % Rotamer: Outliers : 3.12 % Allowed : 20.73 % Favored : 76.15 % 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: -0.17 (0.32), residues: 667 helix: 2.31 (0.35), residues: 209 sheet: -1.08 (0.50), residues: 83 loop : -1.37 (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 0.016 0.001 PHE A 562 TYR 0.014 0.002 TYR B 561 ARG 0.004 0.000 ARG D 496 *********************** 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 92 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8351 (m-30) cc_final: 0.7990 (m-30) REVERT: B 483 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8786 (pp20) REVERT: C 500 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7722 (mp0) REVERT: C 605 ASP cc_start: 0.8624 (t0) cc_final: 0.8091 (m-30) REVERT: C 613 MET cc_start: 0.7107 (mpp) cc_final: 0.5571 (mmt) REVERT: D 488 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8426 (mm) REVERT: D 609 TRP cc_start: 0.6198 (t-100) cc_final: 0.5485 (t-100) REVERT: D 613 MET cc_start: 0.8572 (mpp) cc_final: 0.8062 (mpp) outliers start: 17 outliers final: 15 residues processed: 86 average time/residue: 0.1455 time to fit residues: 18.6446 Evaluate side-chains 88 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 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 597 VAL Chi-restraints excluded: chain C residue 604 VAL 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 610 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 0.0670 chunk 22 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.074577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.052933 restraints weight = 32311.018| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.75 r_work: 0.3134 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.9284 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= 0.233 Angle : 0.717 8.582 11375 Z= 0.395 Chirality : 0.040 0.211 1226 Planarity : 0.007 0.075 1071 Dihedral : 29.420 171.223 2055 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.35 % Favored : 92.35 % Rotamer: Outliers : 2.94 % Allowed : 20.73 % 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: -0.12 (0.32), residues: 667 helix: 2.32 (0.34), residues: 209 sheet: -0.88 (0.50), residues: 80 loop : -1.36 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 464 HIS 0.002 0.000 HIS A 468 PHE 0.018 0.001 PHE A 562 TYR 0.011 0.002 TYR A 518 ARG 0.003 0.000 ARG C 486 ********************** 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 88 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 605 ASP cc_start: 0.8410 (m-30) cc_final: 0.8057 (m-30) REVERT: C 500 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7747 (mp0) REVERT: C 605 ASP cc_start: 0.8663 (t0) cc_final: 0.8123 (m-30) REVERT: C 613 MET cc_start: 0.7146 (mpp) cc_final: 0.5470 (mmt) REVERT: D 488 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8454 (mm) REVERT: D 609 TRP cc_start: 0.6264 (t-100) cc_final: 0.5714 (t-100) REVERT: D 613 MET cc_start: 0.8584 (mpp) cc_final: 0.8087 (mpp) outliers start: 16 outliers final: 15 residues processed: 84 average time/residue: 0.1557 time to fit residues: 19.4863 Evaluate side-chains 85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 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 597 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 597 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.076485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.055174 restraints weight = 32192.325| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.74 r_work: 0.3196 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.9405 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= 0.202 Angle : 0.698 8.791 11375 Z= 0.383 Chirality : 0.040 0.213 1226 Planarity : 0.007 0.065 1071 Dihedral : 29.334 172.981 2055 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.30 % Favored : 93.40 % Rotamer: Outliers : 3.12 % Allowed : 20.92 % Favored : 75.96 % 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: -0.08 (0.32), residues: 667 helix: 2.39 (0.35), residues: 209 sheet: -1.03 (0.50), residues: 83 loop : -1.32 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 464 HIS 0.003 0.000 HIS A 468 PHE 0.015 0.001 PHE C 508 TYR 0.011 0.002 TYR B 561 ARG 0.002 0.000 ARG C 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4641.43 seconds wall clock time: 80 minutes 1.25 seconds (4801.25 seconds total)