Starting phenix.real_space_refine on Sat Apr 6 07:59:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1t_26305/04_2024/7u1t_26305_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1t_26305/04_2024/7u1t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1t_26305/04_2024/7u1t_26305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1t_26305/04_2024/7u1t_26305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1t_26305/04_2024/7u1t_26305_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1t_26305/04_2024/7u1t_26305_neut.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.23, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.48 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: 2.46 Time building geometry restraints manager: 4.89 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: 96.20 - 103.83: 363 103.83 - 111.47: 3815 111.47 - 119.10: 3863 119.10 - 126.73: 2994 126.73 - 134.36: 340 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 2.520 nonbonded pdb=" NH1 ARG C 538 " pdb=" OP1 DA E 21 " model vdw 2.358 2.520 nonbonded pdb=" NH2 ARG D 522 " pdb=" OP2 DT F 46 " model vdw 2.380 2.520 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 2.520 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 454 through 613) selection = (chain 'B' and resid 454 through 613) selection = (chain 'C' and resid 454 through 613) selection = (chain 'D' and resid 454 through 613) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 5.960 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.570 Find NCS groups from input model: 0.400 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- 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 fitting. 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: 0.2477 time to fit residues: 62.8700 Evaluate side-chains 97 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.0070 chunk 69 optimal weight: 3.9990 overall best weight: 0.8006 ------------------------------------------------------------------------------- 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** ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN D 519 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.4464 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= 0.287 Angle : 0.811 9.678 11375 Z= 0.443 Chirality : 0.046 0.211 1226 Planarity : 0.005 0.034 1071 Dihedral : 29.112 168.433 2061 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.75 % Allowed : 4.35 % Favored : 94.90 % Rotamer: Outliers : 4.95 % Allowed : 15.96 % Favored : 79.08 % 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: 2.72 (0.33), residues: 212 sheet: -2.50 (0.49), residues: 80 loop : -1.44 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 464 HIS 0.007 0.001 HIS B 569 PHE 0.018 0.002 PHE D 508 TYR 0.022 0.002 TYR B 510 ARG 0.005 0.001 ARG D 491 *********************** 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 124 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 467 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7715 (mmtt) REVERT: C 613 MET cc_start: 0.3455 (mpp) cc_final: 0.2995 (mpp) REVERT: D 479 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7727 (tm-30) outliers start: 27 outliers final: 14 residues processed: 116 average time/residue: 0.1973 time to fit residues: 30.7819 Evaluate side-chains 89 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 524 THR 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 C residue 441 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 524 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 GLN B 569 HIS C 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.6360 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= 0.274 Angle : 0.756 8.786 11375 Z= 0.418 Chirality : 0.042 0.183 1226 Planarity : 0.006 0.040 1071 Dihedral : 28.821 162.303 2060 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.35 % Favored : 92.35 % Rotamer: Outliers : 6.06 % Allowed : 17.06 % 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: -0.26 (0.32), residues: 667 helix: 2.38 (0.33), residues: 206 sheet: -1.73 (0.51), residues: 79 loop : -1.33 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 464 HIS 0.006 0.001 HIS B 569 PHE 0.020 0.002 PHE A 508 TYR 0.014 0.002 TYR A 518 ARG 0.006 0.001 ARG C 538 *********************** 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 121 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 112 average time/residue: 0.1650 time to fit residues: 26.2366 Evaluate side-chains 98 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 477 LYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 524 THR 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 516 SER Chi-restraints excluded: chain C residue 557 SER 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 524 THR Chi-restraints excluded: chain D residue 541 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.7497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8015 Z= 0.303 Angle : 0.742 8.016 11375 Z= 0.415 Chirality : 0.043 0.175 1226 Planarity : 0.006 0.052 1071 Dihedral : 29.301 158.069 2057 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.50 % Favored : 92.20 % Rotamer: Outliers : 5.32 % Allowed : 18.17 % 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: -0.37 (0.32), residues: 667 helix: 2.21 (0.34), residues: 206 sheet: -1.15 (0.54), residues: 75 loop : -1.53 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 609 HIS 0.009 0.001 HIS B 493 PHE 0.020 0.002 PHE A 562 TYR 0.019 0.002 TYR A 518 ARG 0.007 0.001 ARG C 459 *********************** 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 115 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 563 MET cc_start: 0.7495 (tpp) cc_final: 0.6975 (ttt) REVERT: C 575 LEU cc_start: 0.7798 (tt) cc_final: 0.7525 (tt) REVERT: C 613 MET cc_start: 0.3661 (mpp) cc_final: 0.3271 (mmt) REVERT: D 499 ASP cc_start: 0.7381 (p0) cc_final: 0.7098 (p0) REVERT: D 580 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7531 (tttp) outliers start: 29 outliers final: 23 residues processed: 109 average time/residue: 0.1758 time to fit residues: 27.0305 Evaluate side-chains 101 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 595 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 524 THR 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 597 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 524 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 0.0040 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.7778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8015 Z= 0.227 Angle : 0.690 8.473 11375 Z= 0.386 Chirality : 0.040 0.171 1226 Planarity : 0.006 0.052 1071 Dihedral : 29.104 160.348 2057 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.90 % Favored : 92.80 % Rotamer: Outliers : 3.85 % Allowed : 20.73 % 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: -0.01 (0.33), residues: 667 helix: 2.52 (0.34), residues: 208 sheet: -0.83 (0.54), residues: 81 loop : -1.36 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 609 HIS 0.003 0.001 HIS A 493 PHE 0.020 0.002 PHE C 610 TYR 0.007 0.001 TYR C 561 ARG 0.003 0.000 ARG B 594 *********************** 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 107 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 MET cc_start: 0.7344 (tpp) cc_final: 0.6880 (ttt) REVERT: C 500 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7383 (mp0) REVERT: D 580 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7470 (tttp) outliers start: 21 outliers final: 17 residues processed: 99 average time/residue: 0.1670 time to fit residues: 23.5712 Evaluate side-chains 94 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 507 VAL Chi-restraints excluded: chain B residue 524 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 597 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 524 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.8605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8015 Z= 0.390 Angle : 0.792 7.602 11375 Z= 0.439 Chirality : 0.045 0.163 1226 Planarity : 0.008 0.069 1071 Dihedral : 29.459 162.883 2057 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.85 % Favored : 90.85 % Rotamer: Outliers : 5.69 % Allowed : 17.98 % 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: -0.52 (0.32), residues: 667 helix: 1.82 (0.34), residues: 206 sheet: -0.36 (0.56), residues: 69 loop : -1.64 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 609 HIS 0.003 0.001 HIS C 493 PHE 0.022 0.002 PHE A 562 TYR 0.020 0.003 TYR A 518 ARG 0.005 0.001 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 112 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 563 MET cc_start: 0.7576 (tpp) cc_final: 0.7147 (ttt) REVERT: B 538 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6576 (ptp-170) REVERT: B 580 LYS cc_start: 0.8514 (ttmm) cc_final: 0.7963 (tppt) REVERT: B 592 ASN cc_start: 0.7013 (OUTLIER) cc_final: 0.6472 (p0) REVERT: C 500 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7510 (mp0) REVERT: D 580 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7818 (tttp) outliers start: 31 outliers final: 22 residues processed: 104 average time/residue: 0.1707 time to fit residues: 25.1467 Evaluate side-chains 95 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 561 TYR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 592 ASN 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 524 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.8696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8015 Z= 0.218 Angle : 0.700 8.951 11375 Z= 0.389 Chirality : 0.041 0.186 1226 Planarity : 0.006 0.061 1071 Dihedral : 29.260 166.779 2057 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.60 % Favored : 93.10 % Rotamer: Outliers : 3.12 % Allowed : 21.47 % 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: -0.14 (0.33), residues: 667 helix: 2.39 (0.35), residues: 208 sheet: -0.83 (0.57), residues: 74 loop : -1.43 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 609 HIS 0.002 0.000 HIS A 468 PHE 0.018 0.002 PHE A 562 TYR 0.008 0.001 TYR D 561 ARG 0.002 0.000 ARG C 555 *********************** 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 96 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 563 MET cc_start: 0.7257 (tpp) cc_final: 0.6902 (ttt) REVERT: B 580 LYS cc_start: 0.8385 (ttmm) cc_final: 0.7839 (tppt) REVERT: D 580 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7567 (tttp) outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 0.1620 time to fit residues: 20.7527 Evaluate side-chains 89 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 507 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 597 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 610 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 36 optimal weight: 0.0570 chunk 6 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.8906 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= 0.226 Angle : 0.698 9.795 11375 Z= 0.387 Chirality : 0.040 0.216 1226 Planarity : 0.007 0.061 1071 Dihedral : 29.218 167.047 2055 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.10 % Favored : 91.60 % Rotamer: Outliers : 4.04 % Allowed : 20.73 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: -0.00 (0.33), residues: 667 helix: 2.44 (0.35), residues: 210 sheet: -0.34 (0.59), residues: 69 loop : -1.42 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 609 HIS 0.002 0.000 HIS A 468 PHE 0.019 0.002 PHE A 562 TYR 0.008 0.001 TYR A 518 ARG 0.002 0.000 ARG B 594 *********************** 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 103 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 563 MET cc_start: 0.7295 (tpp) cc_final: 0.6868 (ttt) REVERT: B 580 LYS cc_start: 0.8380 (ttmm) cc_final: 0.7829 (tppt) REVERT: B 592 ASN cc_start: 0.6895 (OUTLIER) cc_final: 0.6337 (p0) REVERT: C 475 ASN cc_start: 0.7547 (m-40) cc_final: 0.7172 (m-40) outliers start: 22 outliers final: 19 residues processed: 95 average time/residue: 0.1720 time to fit residues: 24.2386 Evaluate side-chains 94 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 A residue 605 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 592 ASN 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 524 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 0.0980 chunk 75 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.9312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8015 Z= 0.298 Angle : 0.739 8.610 11375 Z= 0.411 Chirality : 0.042 0.230 1226 Planarity : 0.007 0.057 1071 Dihedral : 29.339 169.052 2055 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.30 % Favored : 90.40 % Rotamer: Outliers : 4.77 % Allowed : 20.37 % 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: -0.34 (0.32), residues: 667 helix: 2.13 (0.35), residues: 206 sheet: -0.52 (0.55), residues: 78 loop : -1.59 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 609 HIS 0.002 0.001 HIS A 493 PHE 0.020 0.002 PHE A 562 TYR 0.014 0.002 TYR A 518 ARG 0.003 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 563 MET cc_start: 0.7494 (tpp) cc_final: 0.7061 (ttt) REVERT: B 580 LYS cc_start: 0.8519 (ttmm) cc_final: 0.7957 (tppt) REVERT: B 592 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6166 (p0) outliers start: 26 outliers final: 22 residues processed: 94 average time/residue: 0.1485 time to fit residues: 20.6111 Evaluate side-chains 95 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 A residue 605 ASP Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 592 ASN 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 494 VAL Chi-restraints excluded: chain D residue 524 THR 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 69 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.0040 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.9421 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= 0.232 Angle : 0.720 10.785 11375 Z= 0.394 Chirality : 0.042 0.304 1226 Planarity : 0.007 0.056 1071 Dihedral : 29.263 171.660 2055 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.95 % Favored : 91.75 % Rotamer: Outliers : 3.67 % Allowed : 22.02 % Favored : 74.31 % 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: -0.22 (0.33), residues: 667 helix: 2.28 (0.35), residues: 209 sheet: -0.42 (0.55), residues: 78 loop : -1.60 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 609 HIS 0.002 0.000 HIS A 468 PHE 0.018 0.002 PHE A 562 TYR 0.009 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 95 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 0.742 Fit side-chains REVERT: A 563 MET cc_start: 0.7309 (tpp) cc_final: 0.6948 (ttt) REVERT: B 580 LYS cc_start: 0.8500 (ttmm) cc_final: 0.7919 (tppt) REVERT: C 613 MET cc_start: 0.3768 (mpp) cc_final: 0.3361 (mmt) outliers start: 20 outliers final: 19 residues processed: 89 average time/residue: 0.1575 time to fit residues: 20.5490 Evaluate side-chains 92 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 A residue 605 ASP Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 499 ASP 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 524 THR 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 60 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.074409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.053110 restraints weight = 31730.924| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.68 r_work: 0.3146 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.9543 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= 0.224 Angle : 0.712 10.579 11375 Z= 0.390 Chirality : 0.041 0.309 1226 Planarity : 0.007 0.059 1071 Dihedral : 29.249 171.884 2055 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.10 % Favored : 91.60 % Rotamer: Outliers : 3.49 % Allowed : 21.83 % Favored : 74.68 % 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: -0.29 (0.33), residues: 667 helix: 2.29 (0.35), residues: 209 sheet: -0.71 (0.53), residues: 84 loop : -1.62 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 609 HIS 0.002 0.000 HIS A 468 PHE 0.018 0.002 PHE A 562 TYR 0.009 0.001 TYR B 510 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: 1860.57 seconds wall clock time: 34 minutes 28.70 seconds (2068.70 seconds total)