Starting phenix.real_space_refine on Tue Feb 13 11:59:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/02_2024/7to0_26025.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/02_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_26025/02_2024/7to0_26025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/02_2024/7to0_26025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/02_2024/7to0_26025.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to0_26025/02_2024/7to0_26025.pdb" } 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 Residue "A GLU 249": "OE1" <-> "OE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 641": "OD1" <-> "OD2" Residue "A ASP 683": "OD1" <-> "OD2" Residue "A ASP 705": "OD1" <-> "OD2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A ASP 802": "OD1" <-> "OD2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 883": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.01, per 1000 atoms: 0.67 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 - 3.50 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 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: 2.04 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: 2.16 Time building geometry restraints manager: 2.54 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: 99.76 - 106.67: 290 106.67 - 113.59: 3380 113.59 - 120.50: 2608 120.50 - 127.41: 2068 127.41 - 134.33: 75 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 2.440 nonbonded pdb=" O GLU A 503 " pdb=" OG1 THR A 506 " model vdw 2.346 2.440 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.364 2.440 nonbonded pdb=" O PHE A 789 " pdb=" OG SER A 793 " model vdw 2.365 2.440 nonbonded pdb=" OD1 ASP A 392 " pdb=" NH2 ARG A 791 " model vdw 2.414 2.520 ... (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 ========== 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.300 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.210 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- 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 : 0.680 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: 0.2182 time to fit residues: 38.8916 Evaluate side-chains 81 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 63 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: A 299 GLN A 305 GLN A 336 GLN A 349 GLN A 353 ASN A 381 HIS A 384 ASN A 501 ASN A 517 GLN A 524 GLN A 608 ASN A 619 GLN A 623 HIS A 769 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6158 Z= 0.185 Angle : 0.512 8.164 8421 Z= 0.252 Chirality : 0.038 0.152 956 Planarity : 0.003 0.030 994 Dihedral : 14.377 73.544 1108 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.45 % Allowed : 15.13 % Favored : 81.41 % 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: -1.44 (0.31), residues: 680 helix: 1.10 (0.29), residues: 307 sheet: -2.79 (0.53), residues: 83 loop : -2.76 (0.30), residues: 290 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 0.025 0.001 PHE A 685 TYR 0.010 0.001 TYR A 715 ARG 0.003 0.000 ARG A 488 *********************** 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 102 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.512 Fit side-chains REVERT: A 279 GLU cc_start: 0.8791 (tp30) cc_final: 0.8493 (tp30) REVERT: A 283 LYS cc_start: 0.8993 (mtpm) cc_final: 0.8707 (mtpp) REVERT: A 321 VAL cc_start: 0.9173 (t) cc_final: 0.8886 (p) REVERT: A 435 ASP cc_start: 0.8535 (t70) cc_final: 0.8309 (t70) REVERT: A 454 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6734 (m-10) REVERT: A 524 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: A 732 ARG cc_start: 0.6741 (ptt90) cc_final: 0.5415 (ptm160) REVERT: A 805 ASN cc_start: 0.7898 (t0) cc_final: 0.7592 (t0) REVERT: A 889 ILE cc_start: 0.9185 (tp) cc_final: 0.8864 (tp) REVERT: A 895 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7545 (tm-30) outliers start: 21 outliers final: 14 residues processed: 93 average time/residue: 0.1757 time to fit residues: 21.7487 Evaluate side-chains 79 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 516 VAL Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 580 ASP 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 Chi-restraints excluded: chain A residue 919 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 353 ASN A 354 ASN A 623 HIS A 678 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2551 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= 0.177 Angle : 0.486 6.634 8421 Z= 0.238 Chirality : 0.038 0.152 956 Planarity : 0.003 0.030 994 Dihedral : 14.182 73.574 1105 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.62 % Allowed : 15.62 % Favored : 80.76 % 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: -0.96 (0.32), residues: 680 helix: 1.68 (0.30), residues: 307 sheet: -2.50 (0.52), residues: 93 loop : -2.74 (0.31), residues: 280 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 0.020 0.001 PHE A 685 TYR 0.010 0.001 TYR A 383 ARG 0.005 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: 22 poor density : 71 time to evaluate : 0.713 Fit side-chains REVERT: A 283 LYS cc_start: 0.9024 (mtpm) cc_final: 0.8481 (mttp) REVERT: A 435 ASP cc_start: 0.8574 (t70) cc_final: 0.8358 (t70) REVERT: A 454 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6750 (m-10) REVERT: A 679 LYS cc_start: 0.7965 (tppt) cc_final: 0.7740 (tttm) REVERT: A 732 ARG cc_start: 0.6779 (ptt90) cc_final: 0.5455 (ptm160) REVERT: A 889 ILE cc_start: 0.9214 (tp) cc_final: 0.8920 (tp) REVERT: A 895 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7481 (tm-30) outliers start: 22 outliers final: 15 residues processed: 85 average time/residue: 0.1541 time to fit residues: 18.3170 Evaluate side-chains 78 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 419 ASN 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 580 ASP 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 766 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 919 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 384 ASN A 557 HIS A 623 HIS A 708 GLN ** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6158 Z= 0.355 Angle : 0.586 7.241 8421 Z= 0.297 Chirality : 0.042 0.219 956 Planarity : 0.004 0.033 994 Dihedral : 14.146 73.397 1105 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.93 % Allowed : 16.12 % Favored : 78.95 % 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: -1.24 (0.32), residues: 680 helix: 1.45 (0.30), residues: 313 sheet: -3.21 (0.44), residues: 104 loop : -2.67 (0.32), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 771 HIS 0.006 0.001 HIS A 623 PHE 0.024 0.002 PHE A 853 TYR 0.013 0.002 TYR A 383 ARG 0.009 0.001 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 96 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 66 time to evaluate : 0.674 Fit side-chains REVERT: A 283 LYS cc_start: 0.9008 (mtpm) cc_final: 0.8806 (mtpp) REVERT: A 425 ASP cc_start: 0.8009 (t0) cc_final: 0.7760 (t0) REVERT: A 454 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: A 620 GLU cc_start: 0.8735 (tp30) cc_final: 0.8272 (tp30) REVERT: A 679 LYS cc_start: 0.8119 (tppt) cc_final: 0.7804 (tttm) REVERT: A 889 ILE cc_start: 0.9252 (tp) cc_final: 0.8985 (tp) outliers start: 30 outliers final: 18 residues processed: 85 average time/residue: 0.1470 time to fit residues: 17.8361 Evaluate side-chains 75 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 419 ASN Chi-restraints excluded: chain A residue 442 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 580 ASP 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 781 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 919 ASP 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: 0.6980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 623 HIS A 754 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6158 Z= 0.172 Angle : 0.490 6.861 8421 Z= 0.244 Chirality : 0.039 0.230 956 Planarity : 0.003 0.031 994 Dihedral : 14.259 73.625 1105 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.28 % Allowed : 17.43 % Favored : 78.29 % 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: -0.75 (0.33), residues: 680 helix: 1.97 (0.31), residues: 307 sheet: -2.91 (0.45), residues: 109 loop : -2.48 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.008 0.001 HIS A 623 PHE 0.014 0.001 PHE A 685 TYR 0.010 0.001 TYR A 383 ARG 0.006 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 89 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 63 time to evaluate : 0.710 Fit side-chains REVERT: A 283 LYS cc_start: 0.8996 (mtpm) cc_final: 0.8794 (mtpp) REVERT: A 425 ASP cc_start: 0.7967 (t0) cc_final: 0.7729 (t0) REVERT: A 454 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: A 620 GLU cc_start: 0.8677 (tp30) cc_final: 0.8137 (tp30) REVERT: A 679 LYS cc_start: 0.8012 (tppt) cc_final: 0.7748 (tttm) REVERT: A 889 ILE cc_start: 0.9265 (tp) cc_final: 0.8982 (tp) outliers start: 26 outliers final: 18 residues processed: 80 average time/residue: 0.1531 time to fit residues: 17.9298 Evaluate side-chains 76 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 419 ASN 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 580 ASP 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 781 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 919 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3424 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= 0.199 Angle : 0.500 6.516 8421 Z= 0.249 Chirality : 0.039 0.238 956 Planarity : 0.003 0.031 994 Dihedral : 14.182 73.598 1105 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.28 % Allowed : 19.41 % Favored : 76.32 % 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: 2.10 (0.31), residues: 307 sheet: -2.85 (0.45), residues: 109 loop : -2.41 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.008 0.001 HIS A 623 PHE 0.014 0.001 PHE A 853 TYR 0.011 0.001 TYR A 383 ARG 0.006 0.000 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 87 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 61 time to evaluate : 0.682 Fit side-chains REVERT: A 283 LYS cc_start: 0.9054 (mtpm) cc_final: 0.8820 (mtpp) REVERT: A 425 ASP cc_start: 0.8006 (t0) cc_final: 0.7756 (t0) REVERT: A 454 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: A 620 GLU cc_start: 0.8700 (tp30) cc_final: 0.8171 (tp30) REVERT: A 679 LYS cc_start: 0.8035 (tppt) cc_final: 0.7801 (tttm) REVERT: A 889 ILE cc_start: 0.9263 (tp) cc_final: 0.9002 (tp) outliers start: 26 outliers final: 18 residues processed: 78 average time/residue: 0.1569 time to fit residues: 17.5363 Evaluate side-chains 75 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 419 ASN 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 580 ASP 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 694 LEU 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 Chi-restraints excluded: chain A residue 919 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6158 Z= 0.288 Angle : 0.554 7.784 8421 Z= 0.277 Chirality : 0.041 0.259 956 Planarity : 0.003 0.036 994 Dihedral : 14.158 73.527 1105 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.44 % Allowed : 19.74 % Favored : 75.82 % 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: -0.81 (0.33), residues: 680 helix: 1.84 (0.30), residues: 313 sheet: -2.97 (0.44), residues: 109 loop : -2.49 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.008 0.001 HIS A 623 PHE 0.020 0.001 PHE A 853 TYR 0.012 0.002 TYR A 383 ARG 0.007 0.001 ARG A 811 *********************** 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 84 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 57 time to evaluate : 0.648 Fit side-chains REVERT: A 283 LYS cc_start: 0.9125 (mtpm) cc_final: 0.8873 (mtpp) REVERT: A 425 ASP cc_start: 0.8055 (t0) cc_final: 0.7802 (t0) REVERT: A 454 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.6837 (m-80) REVERT: A 620 GLU cc_start: 0.8791 (tp30) cc_final: 0.8320 (tp30) REVERT: A 679 LYS cc_start: 0.7960 (tppt) cc_final: 0.7718 (tttt) REVERT: A 889 ILE cc_start: 0.9275 (tp) cc_final: 0.9025 (tp) outliers start: 27 outliers final: 18 residues processed: 75 average time/residue: 0.1416 time to fit residues: 15.3555 Evaluate side-chains 75 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 419 ASN 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 580 ASP 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 694 LEU 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 Chi-restraints excluded: chain A residue 919 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3578 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= 0.197 Angle : 0.512 7.485 8421 Z= 0.254 Chirality : 0.040 0.276 956 Planarity : 0.003 0.032 994 Dihedral : 14.231 73.618 1105 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.28 % Allowed : 19.90 % Favored : 75.82 % 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: -0.58 (0.34), residues: 680 helix: 2.01 (0.31), residues: 313 sheet: -2.72 (0.46), residues: 109 loop : -2.43 (0.34), residues: 258 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 0.011 0.001 TYR A 383 ARG 0.006 0.000 ARG A 811 *********************** 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: 26 poor density : 60 time to evaluate : 0.597 Fit side-chains REVERT: A 283 LYS cc_start: 0.9142 (mtpm) cc_final: 0.8862 (mtpp) REVERT: A 425 ASP cc_start: 0.8006 (t0) cc_final: 0.7756 (t0) REVERT: A 454 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6907 (m-80) REVERT: A 620 GLU cc_start: 0.8732 (tp30) cc_final: 0.8227 (tp30) REVERT: A 822 ASP cc_start: 0.9282 (OUTLIER) cc_final: 0.8684 (p0) REVERT: A 889 ILE cc_start: 0.9253 (tp) cc_final: 0.8990 (tp) outliers start: 26 outliers final: 19 residues processed: 77 average time/residue: 0.1485 time to fit residues: 16.2561 Evaluate side-chains 76 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 419 ASN 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 580 ASP 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 694 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3665 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= 0.233 Angle : 0.536 7.559 8421 Z= 0.266 Chirality : 0.041 0.284 956 Planarity : 0.003 0.034 994 Dihedral : 14.188 73.575 1105 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.77 % Allowed : 19.24 % Favored : 75.99 % 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 (0.34), residues: 680 helix: 1.96 (0.31), residues: 313 sheet: -2.67 (0.47), residues: 109 loop : -2.40 (0.34), residues: 258 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 0.016 0.001 PHE A 853 TYR 0.011 0.001 TYR A 383 ARG 0.008 0.001 ARG A 488 *********************** 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 86 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 57 time to evaluate : 0.696 Fit side-chains REVERT: A 283 LYS cc_start: 0.9116 (mtpm) cc_final: 0.8868 (mtpp) REVERT: A 425 ASP cc_start: 0.8039 (t0) cc_final: 0.7784 (t0) REVERT: A 454 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: A 620 GLU cc_start: 0.8782 (tp30) cc_final: 0.8305 (tp30) REVERT: A 822 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8727 (p0) REVERT: A 889 ILE cc_start: 0.9256 (tp) cc_final: 0.8993 (tp) outliers start: 29 outliers final: 21 residues processed: 76 average time/residue: 0.1380 time to fit residues: 15.3891 Evaluate side-chains 80 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 57 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN 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 419 ASN 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 580 ASP 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 694 LEU Chi-restraints excluded: chain A residue 711 LEU 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: 0.0170 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6158 Z= 0.152 Angle : 0.503 6.842 8421 Z= 0.248 Chirality : 0.039 0.296 956 Planarity : 0.003 0.037 994 Dihedral : 14.198 73.642 1105 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.11 % Allowed : 20.07 % Favored : 75.82 % 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: -0.28 (0.34), residues: 680 helix: 2.27 (0.31), residues: 307 sheet: -2.56 (0.47), residues: 109 loop : -2.18 (0.35), residues: 264 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 0.009 0.001 PHE A 853 TYR 0.010 0.001 TYR A 383 ARG 0.009 0.000 ARG A 488 ********************** 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: 25 poor density : 56 time to evaluate : 0.647 Fit side-chains REVERT: A 249 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8561 (tt0) REVERT: A 283 LYS cc_start: 0.9121 (mtpm) cc_final: 0.8860 (mtpp) REVERT: A 425 ASP cc_start: 0.8006 (t0) cc_final: 0.7773 (t0) REVERT: A 454 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: A 620 GLU cc_start: 0.8724 (tp30) cc_final: 0.8190 (tp30) REVERT: A 822 ASP cc_start: 0.9271 (OUTLIER) cc_final: 0.8729 (p0) REVERT: A 889 ILE cc_start: 0.9226 (tp) cc_final: 0.8958 (tp) outliers start: 25 outliers final: 18 residues processed: 71 average time/residue: 0.1467 time to fit residues: 15.7633 Evaluate side-chains 75 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 419 ASN 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 580 ASP 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 694 LEU 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 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: 3.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 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 349 GLN A 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097882 restraints weight = 8348.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100967 restraints weight = 4934.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102997 restraints weight = 3564.468| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3646 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= 0.208 Angle : 0.524 7.286 8421 Z= 0.259 Chirality : 0.040 0.285 956 Planarity : 0.003 0.036 994 Dihedral : 14.134 73.614 1105 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.95 % Allowed : 20.56 % Favored : 75.49 % 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: -0.41 (0.34), residues: 680 helix: 2.07 (0.31), residues: 313 sheet: -2.53 (0.48), residues: 109 loop : -2.28 (0.35), residues: 258 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 853 TYR 0.013 0.001 TYR A 390 ARG 0.009 0.000 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1412.32 seconds wall clock time: 26 minutes 29.14 seconds (1589.14 seconds total)