Starting phenix.real_space_refine on Tue Sep 24 00:14:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/09_2024/7to0_26025.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/09_2024/7to0_26025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/09_2024/7to0_26025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/09_2024/7to0_26025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/09_2024/7to0_26025.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/09_2024/7to0_26025.cif" } resolution = 3.5 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= 0.004 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 23 5.49 5 S 33 5.16 5 C 3727 2.51 5 N 1027 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5989 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5479 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 653} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 253 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4555 SG CYS A 810 22.813 42.767 28.664 1.00 39.79 S ATOM 4994 SG CYS A 864 21.545 40.805 25.017 1.00 55.33 S ATOM 5033 SG CYS A 869 23.244 44.391 24.842 1.00 53.89 S Time building chain proxies: 4.40, per 1000 atoms: 0.73 Number of scatterers: 5989 At special positions: 0 Unit cell: (97.188, 85.44, 77.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 23 15.00 O 1178 8.00 N 1027 7.00 C 3727 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: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 47.5% alpha, 6.9% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.693A pdb=" N LEU A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 282 removed outlier: 4.041A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.603A pdb=" N GLY A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.697A pdb=" N ASP A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 469 through 488 removed outlier: 3.909A pdb=" N TYR A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 4.150A pdb=" N SER A 497 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.626A pdb=" N VAL A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.591A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 576 Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.689A pdb=" N ASP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 removed outlier: 3.783A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.631A pdb=" N ILE A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.760A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.842A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.293A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.652A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 862 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.80 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: 1640 1.33 - 1.45: 1039 1.45 - 1.58: 3388 1.58 - 1.70: 45 1.70 - 1.82: 46 Bond restraints: 6158 Sorted by residual: bond pdb=" N VAL A 452 " pdb=" CA VAL A 452 " ideal model delta sigma weight residual 1.459 1.494 -0.035 9.10e-03 1.21e+04 1.51e+01 bond pdb=" CA SER A 891 " pdb=" CB SER A 891 " ideal model delta sigma weight residual 1.524 1.486 0.037 1.31e-02 5.83e+03 8.09e+00 bond pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.22e-02 6.72e+03 8.02e+00 bond pdb=" N ILE A 262 " pdb=" CA ILE A 262 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.95e+00 bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.452 1.485 -0.033 1.18e-02 7.18e+03 7.89e+00 ... (remaining 6153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 7073 1.69 - 3.38: 1308 3.38 - 5.07: 36 5.07 - 6.77: 3 6.77 - 8.46: 1 Bond angle restraints: 8421 Sorted by residual: angle pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta sigma weight residual 119.47 127.93 -8.46 1.16e+00 7.43e-01 5.32e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 112.96 107.77 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" N ARG A 316 " pdb=" CA ARG A 316 " pdb=" C ARG A 316 " ideal model delta sigma weight residual 114.75 109.47 5.28 1.26e+00 6.30e-01 1.75e+01 angle pdb=" C THR A 347 " pdb=" CA THR A 347 " pdb=" CB THR A 347 " ideal model delta sigma weight residual 109.31 113.67 -4.36 1.23e+00 6.61e-01 1.26e+01 angle pdb=" N THR A 347 " pdb=" CA THR A 347 " pdb=" C THR A 347 " ideal model delta sigma weight residual 109.62 104.76 4.86 1.45e+00 4.76e-01 1.13e+01 ... (remaining 8416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3347 17.65 - 35.30: 309 35.30 - 52.95: 94 52.95 - 70.60: 35 70.60 - 88.25: 14 Dihedral angle restraints: 3799 sinusoidal: 1797 harmonic: 2002 Sorted by residual: dihedral pdb=" O4' G B 12 " pdb=" C1' G B 12 " pdb=" N9 G B 12 " pdb=" C4 G B 12 " ideal model delta sinusoidal sigma weight residual -106.00 -155.28 49.28 1 1.70e+01 3.46e-03 1.15e+01 dihedral pdb=" CA GLY A 659 " pdb=" C GLY A 659 " pdb=" N ILE A 660 " pdb=" CA ILE A 660 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP A 822 " pdb=" CB ASP A 822 " pdb=" CG ASP A 822 " pdb=" OD1 ASP A 822 " ideal model delta sinusoidal sigma weight residual -30.00 -85.56 55.56 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 3796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 543 0.058 - 0.116: 327 0.116 - 0.174: 84 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 956 Sorted by residual: chirality pdb=" CB VAL A 442 " pdb=" CA VAL A 442 " pdb=" CG1 VAL A 442 " pdb=" CG2 VAL A 442 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB VAL A 453 " pdb=" CA VAL A 453 " pdb=" CG1 VAL A 453 " pdb=" CG2 VAL A 453 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A 780 " pdb=" CA ILE A 780 " pdb=" CG1 ILE A 780 " pdb=" CG2 ILE A 780 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 953 not shown) Planarity restraints: 994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.025 2.00e-02 2.50e+03 1.30e-02 5.09e+00 pdb=" N9 G B 9 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G B 9 " -0.011 2.00e-02 2.50e+03 pdb=" C5 G B 9 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G B 9 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G B 9 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B 9 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 9 " -0.012 2.00e-02 2.50e+03 pdb=" N3 G B 9 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G B 9 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 566 " 0.026 2.00e-02 2.50e+03 1.45e-02 4.18e+00 pdb=" CG TYR A 566 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 566 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 566 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 566 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 566 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 566 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 566 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 7 " -0.024 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N9 A B 7 " 0.018 2.00e-02 2.50e+03 pdb=" C8 A B 7 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 7 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A B 7 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 7 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A B 7 " -0.008 2.00e-02 2.50e+03 pdb=" C2 A B 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 7 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A B 7 " 0.006 2.00e-02 2.50e+03 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1243 2.81 - 3.33: 5567 3.33 - 3.86: 9870 3.86 - 4.38: 11248 4.38 - 4.90: 19078 Nonbonded interactions: 47006 Sorted by model distance: nonbonded pdb=" O LYS A 723 " pdb=" OG1 THR A 727 " model vdw 2.288 3.040 nonbonded pdb=" O GLU A 503 " pdb=" OG1 THR A 506 " model vdw 2.346 3.040 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.364 3.040 nonbonded pdb=" O PHE A 789 " pdb=" OG SER A 793 " model vdw 2.365 3.040 nonbonded pdb=" OD1 ASP A 392 " pdb=" NH2 ARG A 791 " model vdw 2.414 3.120 ... (remaining 47001 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.060 Find NCS groups from input model: 0.060 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.011 0.045 6158 Z= 0.704 Angle : 1.168 8.457 8421 Z= 0.849 Chirality : 0.069 0.290 956 Planarity : 0.004 0.024 994 Dihedral : 16.440 88.252 2499 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.82 % Allowed : 12.66 % Favored : 86.51 % 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: -3.00 (0.27), residues: 680 helix: -0.59 (0.25), residues: 300 sheet: -3.23 (0.48), residues: 90 loop : -3.09 (0.27), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP A 873 HIS 0.010 0.003 HIS A 876 PHE 0.016 0.004 PHE A 388 TYR 0.026 0.004 TYR A 566 ARG 0.008 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 0.643 Fit side-chains REVERT: A 272 PHE cc_start: 0.8675 (t80) cc_final: 0.8435 (t80) REVERT: A 279 GLU cc_start: 0.8652 (tp30) cc_final: 0.8441 (tp30) REVERT: A 283 LYS cc_start: 0.8818 (mtpm) cc_final: 0.8608 (mtpp) REVERT: A 435 ASP cc_start: 0.8367 (t70) cc_final: 0.7873 (t70) REVERT: A 613 ASP cc_start: 0.7795 (t70) cc_final: 0.7566 (t0) REVERT: A 679 LYS cc_start: 0.7585 (tppt) cc_final: 0.7367 (tttt) REVERT: A 732 ARG cc_start: 0.6464 (ptt90) cc_final: 0.5340 (ptm160) REVERT: A 758 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8201 (tm-30) REVERT: A 889 ILE cc_start: 0.8863 (tp) cc_final: 0.8458 (tp) REVERT: A 895 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7778 (tm-30) outliers start: 5 outliers final: 2 residues processed: 142 average time/residue: 0.2192 time to fit residues: 39.1181 Evaluate side-chains 81 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 299 GLN A 305 GLN A 336 GLN A 354 ASN A 381 HIS A 384 ASN A 501 ASN A 517 GLN A 608 ASN A 619 GLN A 623 HIS A 769 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6158 Z= 0.207 Angle : 0.526 7.947 8421 Z= 0.261 Chirality : 0.038 0.144 956 Planarity : 0.003 0.031 994 Dihedral : 14.415 73.562 1108 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.12 % Allowed : 13.82 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.53 (0.31), residues: 680 helix: 1.05 (0.29), residues: 307 sheet: -3.01 (0.48), residues: 99 loop : -2.70 (0.31), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 646 HIS 0.007 0.001 HIS A 623 PHE 0.026 0.002 PHE A 685 TYR 0.011 0.001 TYR A 383 ARG 0.004 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.929 Fit side-chains REVERT: A 283 LYS cc_start: 0.9016 (mtpm) cc_final: 0.8467 (mttp) REVERT: A 435 ASP cc_start: 0.8527 (t70) cc_final: 0.8015 (t70) REVERT: A 454 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6803 (m-10) REVERT: A 477 GLN cc_start: 0.7915 (tp40) cc_final: 0.7597 (tp40) REVERT: A 622 TYR cc_start: 0.8880 (m-80) cc_final: 0.8649 (m-10) REVERT: A 732 ARG cc_start: 0.6727 (ptt90) cc_final: 0.5420 (ptm160) REVERT: A 754 ASN cc_start: 0.7709 (m-40) cc_final: 0.7493 (m-40) REVERT: A 758 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 805 ASN cc_start: 0.7891 (t0) cc_final: 0.7582 (t0) REVERT: A 889 ILE cc_start: 0.9206 (tp) cc_final: 0.8905 (tp) REVERT: A 895 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7547 (tm-30) outliers start: 19 outliers final: 13 residues processed: 94 average time/residue: 0.1662 time to fit residues: 21.1530 Evaluate side-chains 82 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS A 623 HIS A 678 GLN A 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6158 Z= 0.212 Angle : 0.510 7.067 8421 Z= 0.253 Chirality : 0.038 0.140 956 Planarity : 0.003 0.032 994 Dihedral : 14.198 73.591 1105 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.45 % Allowed : 13.32 % Favored : 83.22 % 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: -1.01 (0.32), residues: 680 helix: 1.62 (0.30), residues: 307 sheet: -3.15 (0.49), residues: 92 loop : -2.47 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 512 HIS 0.007 0.001 HIS A 623 PHE 0.020 0.001 PHE A 685 TYR 0.011 0.001 TYR A 383 ARG 0.007 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.719 Fit side-chains REVERT: A 277 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8915 (mp) REVERT: A 283 LYS cc_start: 0.8902 (mtpm) cc_final: 0.8690 (mtpp) REVERT: A 425 ASP cc_start: 0.7989 (t0) cc_final: 0.7745 (t0) REVERT: A 454 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6809 (m-10) REVERT: A 477 GLN cc_start: 0.7997 (tp40) cc_final: 0.7736 (tp40) REVERT: A 584 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: A 620 GLU cc_start: 0.8607 (tp30) cc_final: 0.8067 (tp30) REVERT: A 679 LYS cc_start: 0.7975 (tppt) cc_final: 0.7743 (tttm) REVERT: A 758 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8310 (tm-30) REVERT: A 889 ILE cc_start: 0.9236 (tp) cc_final: 0.8935 (tp) REVERT: A 895 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7703 (tm-30) outliers start: 21 outliers final: 12 residues processed: 85 average time/residue: 0.1597 time to fit residues: 19.5006 Evaluate side-chains 77 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6158 Z= 0.197 Angle : 0.502 6.762 8421 Z= 0.251 Chirality : 0.039 0.216 956 Planarity : 0.003 0.032 994 Dihedral : 14.208 73.603 1105 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.45 % Allowed : 14.64 % Favored : 81.91 % 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: -0.78 (0.33), residues: 680 helix: 1.87 (0.30), residues: 307 sheet: -3.14 (0.49), residues: 88 loop : -2.43 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.007 0.001 HIS A 623 PHE 0.017 0.001 PHE A 685 TYR 0.012 0.001 TYR A 622 ARG 0.006 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.617 Fit side-chains REVERT: A 283 LYS cc_start: 0.8947 (mtpm) cc_final: 0.8742 (mtpp) REVERT: A 425 ASP cc_start: 0.7986 (t0) cc_final: 0.7757 (t0) REVERT: A 454 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6905 (m-80) REVERT: A 477 GLN cc_start: 0.8047 (tp40) cc_final: 0.7794 (tp40) REVERT: A 655 PHE cc_start: 0.8803 (p90) cc_final: 0.8467 (p90) REVERT: A 679 LYS cc_start: 0.7984 (tppt) cc_final: 0.7745 (tttm) REVERT: A 754 ASN cc_start: 0.7644 (m-40) cc_final: 0.7368 (m-40) REVERT: A 758 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8310 (tm-30) REVERT: A 889 ILE cc_start: 0.9248 (tp) cc_final: 0.8960 (tp) REVERT: A 895 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7631 (tm-30) outliers start: 21 outliers final: 14 residues processed: 84 average time/residue: 0.1485 time to fit residues: 17.4561 Evaluate side-chains 75 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6158 Z= 0.154 Angle : 0.482 6.660 8421 Z= 0.238 Chirality : 0.038 0.230 956 Planarity : 0.003 0.031 994 Dihedral : 14.166 73.611 1105 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.45 % Allowed : 15.30 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.33), residues: 680 helix: 2.09 (0.30), residues: 307 sheet: -3.02 (0.49), residues: 88 loop : -2.36 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.007 0.001 HIS A 623 PHE 0.014 0.001 PHE A 685 TYR 0.009 0.001 TYR A 715 ARG 0.008 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.635 Fit side-chains REVERT: A 283 LYS cc_start: 0.9019 (mtpm) cc_final: 0.8806 (mtpp) REVERT: A 425 ASP cc_start: 0.7984 (t0) cc_final: 0.7751 (t0) REVERT: A 454 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: A 477 GLN cc_start: 0.8123 (tp40) cc_final: 0.7910 (tp40) REVERT: A 679 LYS cc_start: 0.7997 (tppt) cc_final: 0.7712 (tttm) REVERT: A 754 ASN cc_start: 0.7627 (m-40) cc_final: 0.7400 (m-40) REVERT: A 758 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8294 (tm-30) REVERT: A 777 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7743 (mmt90) REVERT: A 889 ILE cc_start: 0.9228 (tp) cc_final: 0.8941 (tp) REVERT: A 895 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7688 (tm-30) outliers start: 21 outliers final: 12 residues processed: 78 average time/residue: 0.1582 time to fit residues: 17.2514 Evaluate side-chains 73 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 49 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: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 6158 Z= 0.432 Angle : 0.641 7.601 8421 Z= 0.322 Chirality : 0.044 0.240 956 Planarity : 0.004 0.037 994 Dihedral : 14.074 73.379 1105 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.28 % Allowed : 16.45 % Favored : 79.28 % 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: -1.04 (0.32), residues: 680 helix: 1.59 (0.30), residues: 313 sheet: -3.13 (0.44), residues: 103 loop : -2.54 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 771 HIS 0.008 0.001 HIS A 623 PHE 0.026 0.002 PHE A 853 TYR 0.013 0.002 TYR A 383 ARG 0.008 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 0.510 Fit side-chains REVERT: A 283 LYS cc_start: 0.9132 (mtpm) cc_final: 0.8893 (mtpp) REVERT: A 425 ASP cc_start: 0.8093 (t0) cc_final: 0.7828 (t0) REVERT: A 454 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: A 479 MET cc_start: 0.8290 (mtm) cc_final: 0.7869 (mtm) REVERT: A 620 GLU cc_start: 0.8825 (tp30) cc_final: 0.8392 (tp30) REVERT: A 679 LYS cc_start: 0.8038 (tppt) cc_final: 0.7698 (ttpp) REVERT: A 758 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 889 ILE cc_start: 0.9285 (tp) cc_final: 0.9025 (tp) outliers start: 26 outliers final: 12 residues processed: 80 average time/residue: 0.1403 time to fit residues: 15.6022 Evaluate side-chains 67 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6158 Z= 0.193 Angle : 0.519 7.163 8421 Z= 0.260 Chirality : 0.040 0.267 956 Planarity : 0.003 0.034 994 Dihedral : 14.256 73.623 1105 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.45 % Allowed : 17.93 % Favored : 78.62 % 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: -0.60 (0.33), residues: 680 helix: 2.03 (0.30), residues: 307 sheet: -3.12 (0.44), residues: 98 loop : -2.26 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.009 0.001 HIS A 623 PHE 0.014 0.001 PHE A 459 TYR 0.029 0.001 TYR A 622 ARG 0.007 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 0.624 Fit side-chains REVERT: A 283 LYS cc_start: 0.9123 (mtpm) cc_final: 0.8880 (mtpp) REVERT: A 425 ASP cc_start: 0.8006 (t0) cc_final: 0.7740 (t0) REVERT: A 454 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: A 620 GLU cc_start: 0.8779 (tp30) cc_final: 0.8243 (tp30) REVERT: A 655 PHE cc_start: 0.8927 (p90) cc_final: 0.8718 (p90) REVERT: A 679 LYS cc_start: 0.7913 (tppt) cc_final: 0.7673 (tttm) REVERT: A 754 ASN cc_start: 0.7605 (m-40) cc_final: 0.7348 (m-40) REVERT: A 758 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8340 (tm-30) REVERT: A 889 ILE cc_start: 0.9260 (tp) cc_final: 0.9003 (tp) outliers start: 21 outliers final: 14 residues processed: 78 average time/residue: 0.1489 time to fit residues: 16.4308 Evaluate side-chains 75 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6158 Z= 0.199 Angle : 0.522 6.853 8421 Z= 0.259 Chirality : 0.040 0.274 956 Planarity : 0.003 0.035 994 Dihedral : 14.182 73.608 1105 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.45 % Allowed : 18.91 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.34), residues: 680 helix: 1.98 (0.30), residues: 313 sheet: -2.97 (0.46), residues: 98 loop : -2.26 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.009 0.001 HIS A 623 PHE 0.014 0.001 PHE A 853 TYR 0.028 0.001 TYR A 622 ARG 0.006 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.676 Fit side-chains REVERT: A 283 LYS cc_start: 0.9125 (mtpm) cc_final: 0.8880 (mtpp) REVERT: A 425 ASP cc_start: 0.8021 (t0) cc_final: 0.7762 (t0) REVERT: A 454 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: A 620 GLU cc_start: 0.8741 (tp30) cc_final: 0.8218 (tp30) REVERT: A 679 LYS cc_start: 0.7848 (tppt) cc_final: 0.7618 (tttm) REVERT: A 754 ASN cc_start: 0.7679 (m-40) cc_final: 0.7406 (m-40) REVERT: A 758 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8326 (tm-30) REVERT: A 822 ASP cc_start: 0.9288 (OUTLIER) cc_final: 0.8313 (p0) REVERT: A 889 ILE cc_start: 0.9289 (tp) cc_final: 0.9035 (tp) REVERT: A 895 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7777 (tm-30) outliers start: 21 outliers final: 14 residues processed: 77 average time/residue: 0.1507 time to fit residues: 16.6620 Evaluate side-chains 74 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 919 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6158 Z= 0.247 Angle : 0.549 8.411 8421 Z= 0.272 Chirality : 0.041 0.288 956 Planarity : 0.004 0.035 994 Dihedral : 14.142 73.539 1105 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.78 % Allowed : 18.26 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.33), residues: 680 helix: 1.92 (0.30), residues: 313 sheet: -2.96 (0.46), residues: 98 loop : -2.27 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.009 0.001 HIS A 623 PHE 0.017 0.001 PHE A 853 TYR 0.020 0.002 TYR A 622 ARG 0.007 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 59 time to evaluate : 0.679 Fit side-chains REVERT: A 283 LYS cc_start: 0.9134 (mtpm) cc_final: 0.8882 (mtpp) REVERT: A 425 ASP cc_start: 0.8068 (t0) cc_final: 0.7802 (t0) REVERT: A 454 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: A 679 LYS cc_start: 0.7904 (tppt) cc_final: 0.7669 (tttm) REVERT: A 754 ASN cc_start: 0.7692 (m-40) cc_final: 0.7411 (m-40) REVERT: A 758 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 822 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.8264 (p0) REVERT: A 889 ILE cc_start: 0.9268 (tp) cc_final: 0.9022 (tp) outliers start: 23 outliers final: 16 residues processed: 73 average time/residue: 0.1599 time to fit residues: 16.2945 Evaluate side-chains 74 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 919 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6158 Z= 0.213 Angle : 0.539 8.442 8421 Z= 0.266 Chirality : 0.040 0.283 956 Planarity : 0.003 0.035 994 Dihedral : 14.157 73.618 1105 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.12 % Allowed : 19.08 % Favored : 77.80 % 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: -0.55 (0.33), residues: 680 helix: 1.99 (0.30), residues: 312 sheet: -2.98 (0.45), residues: 98 loop : -2.24 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.010 0.001 HIS A 623 PHE 0.015 0.001 PHE A 655 TYR 0.022 0.001 TYR A 622 ARG 0.006 0.000 ARG A 811 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 0.675 Fit side-chains REVERT: A 283 LYS cc_start: 0.9138 (mtpm) cc_final: 0.8886 (mtpp) REVERT: A 425 ASP cc_start: 0.8024 (t0) cc_final: 0.7768 (t0) REVERT: A 454 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: A 679 LYS cc_start: 0.7858 (tppt) cc_final: 0.7626 (tttm) REVERT: A 754 ASN cc_start: 0.7612 (m-40) cc_final: 0.7338 (m-40) REVERT: A 758 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8321 (tm-30) REVERT: A 822 ASP cc_start: 0.9289 (OUTLIER) cc_final: 0.8281 (p0) REVERT: A 889 ILE cc_start: 0.9269 (tp) cc_final: 0.9023 (tp) REVERT: A 895 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7703 (tm-30) outliers start: 19 outliers final: 15 residues processed: 73 average time/residue: 0.1479 time to fit residues: 15.5096 Evaluate side-chains 76 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 919 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098998 restraints weight = 8331.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102145 restraints weight = 4746.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104179 restraints weight = 3354.484| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6158 Z= 0.183 Angle : 0.528 8.087 8421 Z= 0.261 Chirality : 0.040 0.277 956 Planarity : 0.003 0.035 994 Dihedral : 14.139 73.624 1105 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.29 % Allowed : 18.75 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.40 (0.34), residues: 680 helix: 2.18 (0.31), residues: 306 sheet: -2.65 (0.45), residues: 108 loop : -2.21 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.010 0.001 HIS A 623 PHE 0.015 0.001 PHE A 655 TYR 0.020 0.001 TYR A 622 ARG 0.006 0.000 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1331.31 seconds wall clock time: 35 minutes 5.09 seconds (2105.09 seconds total)