Starting phenix.real_space_refine on Tue Jan 14 08:44:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tny_26023/01_2025/7tny_26023.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tny_26023/01_2025/7tny_26023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tny_26023/01_2025/7tny_26023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tny_26023/01_2025/7tny_26023.map" model { file = "/net/cci-nas-00/data/ceres_data/7tny_26023/01_2025/7tny_26023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tny_26023/01_2025/7tny_26023.cif" } resolution = 3.2 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 25 5.49 5 S 33 5.16 5 C 3654 2.51 5 N 996 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5865 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5347 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'GDP': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GDP B 1 " pdbres=" G B 2 " 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 4423 SG CYS A 810 69.001 56.638 22.800 1.00 29.85 S ATOM 4862 SG CYS A 864 68.607 55.061 18.956 1.00 41.61 S ATOM 4901 SG CYS A 869 70.871 53.767 21.505 1.00 42.96 S Time building chain proxies: 4.19, per 1000 atoms: 0.71 Number of scatterers: 5865 At special positions: 0 Unit cell: (100.392, 85.44, 80.1, 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 25 15.00 O 1156 8.00 N 996 7.00 C 3654 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 799.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1274 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 48.5% alpha, 9.3% beta 8 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.522A pdb=" N GLY A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 284 removed outlier: 3.790A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 339 Processing helix chain 'A' and resid 347 through 358 removed outlier: 4.237A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.868A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 381 through 396 removed outlier: 3.636A pdb=" N GLN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.916A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 488 removed outlier: 3.769A pdb=" N ARG A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.896A pdb=" N GLU A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 511 " --> pdb=" O GLN A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.750A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.871A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.796A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 removed outlier: 3.514A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.656A pdb=" N GLU A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 4.003A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.511A pdb=" N LEU A 682 " --> pdb=" O GLN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.526A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 759 " --> pdb=" O MET A 755 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 removed outlier: 4.306A pdb=" N HIS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 892 Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.417A pdb=" N VAL A 293 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A 346 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 295 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460 removed outlier: 7.036A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.531A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.755A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.82 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: 1703 1.33 - 1.46: 918 1.46 - 1.58: 3316 1.58 - 1.70: 47 1.70 - 1.82: 46 Bond restraints: 6030 Sorted by residual: bond pdb=" CA SER A 654 " pdb=" CB SER A 654 " ideal model delta sigma weight residual 1.536 1.491 0.045 1.42e-02 4.96e+03 1.00e+01 bond pdb=" N VAL A 453 " pdb=" CA VAL A 453 " ideal model delta sigma weight residual 1.460 1.487 -0.027 8.60e-03 1.35e+04 9.57e+00 bond pdb=" C GLY A 663 " pdb=" O GLY A 663 " ideal model delta sigma weight residual 1.229 1.254 -0.024 8.20e-03 1.49e+04 8.73e+00 bond pdb=" N ILE A 725 " pdb=" CA ILE A 725 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.19e-02 7.06e+03 8.68e+00 bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.66e+00 ... (remaining 6025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 6346 1.39 - 2.79: 1790 2.79 - 4.18: 98 4.18 - 5.57: 10 5.57 - 6.97: 3 Bond angle restraints: 8247 Sorted by residual: angle pdb=" N VAL A 453 " pdb=" CA VAL A 453 " pdb=" C VAL A 453 " ideal model delta sigma weight residual 113.71 108.29 5.42 9.50e-01 1.11e+00 3.25e+01 angle pdb=" N ILE A 489 " pdb=" CA ILE A 489 " pdb=" C ILE A 489 " ideal model delta sigma weight residual 111.45 108.11 3.34 9.30e-01 1.16e+00 1.29e+01 angle pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta sigma weight residual 119.24 122.84 -3.60 1.04e+00 9.25e-01 1.20e+01 angle pdb=" N ASP A 529 " pdb=" CA ASP A 529 " pdb=" C ASP A 529 " ideal model delta sigma weight residual 113.43 109.11 4.32 1.26e+00 6.30e-01 1.17e+01 angle pdb=" CA VAL A 414 " pdb=" C VAL A 414 " pdb=" O VAL A 414 " ideal model delta sigma weight residual 120.30 117.38 2.92 9.40e-01 1.13e+00 9.65e+00 ... (remaining 8242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3299 17.71 - 35.42: 280 35.42 - 53.13: 81 53.13 - 70.84: 30 70.84 - 88.55: 19 Dihedral angle restraints: 3709 sinusoidal: 1752 harmonic: 1957 Sorted by residual: dihedral pdb=" CA PHE A 853 " pdb=" C PHE A 853 " pdb=" N SER A 854 " pdb=" CA SER A 854 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" O4' C C 13 " pdb=" C1' C C 13 " pdb=" N1 C C 13 " pdb=" C2 C C 13 " ideal model delta sinusoidal sigma weight residual -160.00 -115.80 -44.20 1 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CA GLY A 358 " pdb=" C GLY A 358 " pdb=" N THR A 359 " pdb=" CA THR A 359 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 3706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 388 0.038 - 0.076: 278 0.076 - 0.114: 199 0.114 - 0.152: 65 0.152 - 0.190: 9 Chirality restraints: 939 Sorted by residual: chirality pdb=" P G B 2 " pdb=" OP1 G B 2 " pdb=" OP2 G B 2 " pdb=" O5' G B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.22 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" C2' G C 14 " pdb=" C3' G C 14 " pdb=" O2' G C 14 " pdb=" C1' G C 14 " both_signs ideal model delta sigma weight residual False -2.75 -2.57 -0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" C2' G B 12 " pdb=" C3' G B 12 " pdb=" O2' G B 12 " pdb=" C1' G B 12 " both_signs ideal model delta sigma weight residual False -2.75 -2.57 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 936 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 19 " 0.020 2.00e-02 2.50e+03 8.51e-03 1.99e+00 pdb=" N9 A C 19 " -0.009 2.00e-02 2.50e+03 pdb=" C8 A C 19 " -0.009 2.00e-02 2.50e+03 pdb=" N7 A C 19 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A C 19 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A C 19 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A C 19 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A C 19 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A C 19 " -0.010 2.00e-02 2.50e+03 pdb=" N3 A C 19 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A C 19 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 697 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C THR A 697 " 0.023 2.00e-02 2.50e+03 pdb=" O THR A 697 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 698 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 5 " -0.013 2.00e-02 2.50e+03 7.52e-03 1.70e+00 pdb=" N9 G B 5 " -0.002 2.00e-02 2.50e+03 pdb=" C8 G B 5 " 0.010 2.00e-02 2.50e+03 pdb=" N7 G B 5 " 0.013 2.00e-02 2.50e+03 pdb=" C5 G B 5 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G B 5 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G B 5 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 5 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 5 " 0.008 2.00e-02 2.50e+03 pdb=" N2 G B 5 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G B 5 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 5 " -0.002 2.00e-02 2.50e+03 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1461 2.82 - 3.34: 5630 3.34 - 3.86: 9571 3.86 - 4.38: 11184 4.38 - 4.90: 18702 Nonbonded interactions: 46548 Sorted by model distance: nonbonded pdb=" O LYS A 379 " pdb=" OP1 G B 5 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 362 " pdb=" OG SER A 364 " model vdw 2.355 3.040 nonbonded pdb=" O GLU A 503 " pdb=" OG1 THR A 506 " model vdw 2.364 3.040 nonbonded pdb=" N ASP A 580 " pdb=" OD1 ASP A 580 " model vdw 2.365 3.120 nonbonded pdb=" OE2 GLU A 531 " pdb=" NZ LYS A 814 " model vdw 2.422 3.120 ... (remaining 46543 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.880 Find NCS groups from input model: 0.070 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 0.052 6030 Z= 0.695 Angle : 1.143 6.967 8247 Z= 0.833 Chirality : 0.067 0.190 939 Planarity : 0.004 0.021 965 Dihedral : 16.383 88.548 2435 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.84 % Allowed : 8.60 % Favored : 90.56 % 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: -3.18 (0.29), residues: 658 helix: -0.79 (0.29), residues: 281 sheet: -3.50 (0.47), residues: 81 loop : -3.01 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 873 HIS 0.013 0.002 HIS A 876 PHE 0.016 0.003 PHE A 853 TYR 0.015 0.003 TYR A 548 ARG 0.006 0.001 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.686 Fit side-chains REVERT: A 446 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6489 (mm) REVERT: A 492 ASP cc_start: 0.8066 (p0) cc_final: 0.7727 (p0) REVERT: A 588 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 724 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.5834 (tmm) outliers start: 5 outliers final: 2 residues processed: 124 average time/residue: 0.2383 time to fit residues: 36.6520 Evaluate side-chains 80 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 305 GLN A 340 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS A 902 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111130 restraints weight = 7379.048| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.20 r_work: 0.3128 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6030 Z= 0.197 Angle : 0.527 6.677 8247 Z= 0.263 Chirality : 0.040 0.182 939 Planarity : 0.003 0.033 965 Dihedral : 14.190 73.649 1086 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.18 % Allowed : 14.84 % Favored : 83.98 % 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: -1.73 (0.32), residues: 658 helix: 0.78 (0.31), residues: 289 sheet: -3.03 (0.51), residues: 79 loop : -2.67 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.003 0.001 HIS A 623 PHE 0.027 0.001 PHE A 616 TYR 0.012 0.001 TYR A 566 ARG 0.006 0.001 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.621 Fit side-chains REVERT: A 312 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8278 (mttp) REVERT: A 336 GLN cc_start: 0.8389 (mm110) cc_final: 0.8091 (mm-40) REVERT: A 435 ASP cc_start: 0.8834 (t0) cc_final: 0.8599 (t0) REVERT: A 446 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6905 (mm) REVERT: A 492 ASP cc_start: 0.7978 (p0) cc_final: 0.7778 (p0) REVERT: A 523 PHE cc_start: 0.8571 (t80) cc_final: 0.8329 (t80) REVERT: A 602 ARG cc_start: 0.7723 (ttt180) cc_final: 0.7413 (ptt180) REVERT: A 620 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7019 (mt-10) REVERT: A 673 MET cc_start: 0.6702 (ttt) cc_final: 0.6288 (mtp) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.1714 time to fit residues: 21.2171 Evaluate side-chains 80 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 298 ASN A 375 HIS A 691 HIS ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104987 restraints weight = 7494.563| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.14 r_work: 0.3071 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6030 Z= 0.242 Angle : 0.538 7.338 8247 Z= 0.269 Chirality : 0.040 0.194 939 Planarity : 0.003 0.038 965 Dihedral : 14.126 73.621 1080 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.70 % Allowed : 15.85 % Favored : 81.45 % 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: -1.21 (0.33), residues: 658 helix: 1.22 (0.31), residues: 296 sheet: -2.72 (0.50), residues: 87 loop : -2.47 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 646 HIS 0.002 0.001 HIS A 623 PHE 0.029 0.001 PHE A 616 TYR 0.007 0.001 TYR A 303 ARG 0.006 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.670 Fit side-chains REVERT: A 336 GLN cc_start: 0.8444 (mm110) cc_final: 0.8098 (mm-40) REVERT: A 435 ASP cc_start: 0.8933 (t0) cc_final: 0.8581 (t0) REVERT: A 620 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7137 (mt-10) REVERT: A 859 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8445 (mtt-85) REVERT: A 882 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7685 (p90) REVERT: A 883 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7911 (mp0) outliers start: 16 outliers final: 11 residues processed: 87 average time/residue: 0.1589 time to fit residues: 19.0812 Evaluate side-chains 79 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.103716 restraints weight = 7708.603| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.17 r_work: 0.3063 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6030 Z= 0.199 Angle : 0.516 7.352 8247 Z= 0.258 Chirality : 0.039 0.194 939 Planarity : 0.003 0.039 965 Dihedral : 14.082 73.636 1080 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.70 % Allowed : 15.85 % Favored : 81.45 % 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: -1.00 (0.33), residues: 658 helix: 1.35 (0.32), residues: 299 sheet: -2.63 (0.50), residues: 87 loop : -2.36 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.002 0.001 HIS A 375 PHE 0.029 0.001 PHE A 616 TYR 0.009 0.001 TYR A 390 ARG 0.005 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.646 Fit side-chains REVERT: A 336 GLN cc_start: 0.8383 (mm110) cc_final: 0.8058 (mm-40) REVERT: A 435 ASP cc_start: 0.8958 (t0) cc_final: 0.8593 (t0) REVERT: A 616 PHE cc_start: 0.8373 (t80) cc_final: 0.7978 (t80) REVERT: A 620 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7574 (mt-10) REVERT: A 724 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6004 (tmm) REVERT: A 882 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7568 (p90) REVERT: A 883 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7864 (mp0) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.1519 time to fit residues: 17.4046 Evaluate side-chains 79 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104368 restraints weight = 7528.722| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.15 r_work: 0.3080 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6030 Z= 0.192 Angle : 0.514 7.754 8247 Z= 0.256 Chirality : 0.039 0.209 939 Planarity : 0.003 0.038 965 Dihedral : 13.932 73.622 1080 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.20 % Allowed : 16.53 % Favored : 80.27 % 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: -0.86 (0.33), residues: 658 helix: 1.38 (0.32), residues: 305 sheet: -3.16 (0.52), residues: 62 loop : -2.19 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 375 PHE 0.024 0.001 PHE A 616 TYR 0.010 0.001 TYR A 390 ARG 0.008 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.8982 (t0) cc_final: 0.8597 (t0) REVERT: A 724 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6261 (tmm) REVERT: A 882 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7468 (p90) REVERT: A 883 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7947 (mp0) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.1541 time to fit residues: 18.3169 Evaluate side-chains 81 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 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 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109039 restraints weight = 7376.163| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.99 r_work: 0.3135 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6030 Z= 0.198 Angle : 0.515 7.679 8247 Z= 0.258 Chirality : 0.039 0.180 939 Planarity : 0.003 0.038 965 Dihedral : 13.880 73.622 1080 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.20 % Allowed : 17.71 % Favored : 79.09 % 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: -0.79 (0.33), residues: 658 helix: 1.48 (0.32), residues: 303 sheet: -2.54 (0.51), residues: 87 loop : -2.23 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 375 PHE 0.017 0.001 PHE A 616 TYR 0.010 0.001 TYR A 390 ARG 0.010 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.686 Fit side-chains REVERT: A 435 ASP cc_start: 0.9011 (t0) cc_final: 0.8646 (t0) REVERT: A 621 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7797 (mm-30) REVERT: A 724 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6427 (tmm) REVERT: A 882 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7398 (p90) outliers start: 19 outliers final: 13 residues processed: 83 average time/residue: 0.1395 time to fit residues: 16.5277 Evaluate side-chains 79 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105343 restraints weight = 7570.683| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.03 r_work: 0.3079 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6030 Z= 0.296 Angle : 0.565 8.149 8247 Z= 0.285 Chirality : 0.041 0.188 939 Planarity : 0.004 0.040 965 Dihedral : 13.829 73.648 1080 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.54 % Allowed : 17.71 % Favored : 78.75 % 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: -0.76 (0.34), residues: 658 helix: 1.53 (0.32), residues: 299 sheet: -2.65 (0.51), residues: 88 loop : -2.14 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.003 0.001 HIS A 375 PHE 0.025 0.001 PHE A 616 TYR 0.009 0.001 TYR A 390 ARG 0.012 0.001 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.9057 (t0) cc_final: 0.8626 (t0) REVERT: A 724 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6627 (tmm) REVERT: A 882 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7680 (p90) outliers start: 21 outliers final: 16 residues processed: 84 average time/residue: 0.1461 time to fit residues: 17.6128 Evaluate side-chains 84 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.0370 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 36 optimal weight: 0.0040 chunk 1 optimal weight: 1.9990 overall best weight: 0.3268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107446 restraints weight = 7443.194| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.11 r_work: 0.3091 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6030 Z= 0.141 Angle : 0.499 6.636 8247 Z= 0.253 Chirality : 0.038 0.151 939 Planarity : 0.003 0.037 965 Dihedral : 13.885 73.617 1080 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.04 % Allowed : 17.88 % Favored : 79.09 % 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: -0.63 (0.34), residues: 658 helix: 1.59 (0.31), residues: 303 sheet: -2.43 (0.52), residues: 87 loop : -2.13 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 771 HIS 0.002 0.001 HIS A 623 PHE 0.025 0.001 PHE A 616 TYR 0.011 0.001 TYR A 509 ARG 0.012 0.001 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.8971 (t0) cc_final: 0.8584 (t0) REVERT: A 616 PHE cc_start: 0.8256 (t80) cc_final: 0.7814 (t80) REVERT: A 620 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 621 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 724 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6588 (tmm) REVERT: A 882 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7159 (p90) outliers start: 18 outliers final: 13 residues processed: 81 average time/residue: 0.1552 time to fit residues: 17.5763 Evaluate side-chains 79 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 315 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105321 restraints weight = 7533.253| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.12 r_work: 0.3074 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6030 Z= 0.201 Angle : 0.528 7.076 8247 Z= 0.267 Chirality : 0.039 0.178 939 Planarity : 0.003 0.038 965 Dihedral : 13.829 73.615 1080 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.53 % Allowed : 19.06 % Favored : 78.41 % 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: -0.58 (0.34), residues: 658 helix: 1.61 (0.31), residues: 304 sheet: -2.48 (0.51), residues: 88 loop : -2.05 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 623 PHE 0.023 0.001 PHE A 616 TYR 0.012 0.001 TYR A 390 ARG 0.012 0.001 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.8974 (t0) cc_final: 0.8561 (t0) REVERT: A 620 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7155 (mt-10) REVERT: A 621 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7646 (mm-30) REVERT: A 673 MET cc_start: 0.6443 (ttt) cc_final: 0.5971 (mtp) REVERT: A 724 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6678 (tmm) REVERT: A 882 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7250 (p90) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1576 time to fit residues: 17.5291 Evaluate side-chains 77 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 315 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 0.0050 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104807 restraints weight = 7523.949| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.11 r_work: 0.3058 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6030 Z= 0.209 Angle : 0.534 7.036 8247 Z= 0.271 Chirality : 0.039 0.171 939 Planarity : 0.003 0.039 965 Dihedral : 13.836 73.610 1080 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.53 % Allowed : 19.56 % Favored : 77.91 % 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: -0.48 (0.34), residues: 658 helix: 1.68 (0.31), residues: 303 sheet: -2.39 (0.52), residues: 87 loop : -2.00 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 375 PHE 0.022 0.001 PHE A 616 TYR 0.011 0.001 TYR A 390 ARG 0.013 0.001 ARG A 859 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.8971 (t0) cc_final: 0.8537 (t0) REVERT: A 620 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7069 (mt-10) REVERT: A 621 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7605 (mm-30) REVERT: A 673 MET cc_start: 0.6323 (ttt) cc_final: 0.5820 (mtp) REVERT: A 724 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6654 (tmm) REVERT: A 882 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7281 (p90) outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 0.1443 time to fit residues: 15.3984 Evaluate side-chains 76 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 315 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.3003 > 50: distance: 27 - 28: 12.559 distance: 27 - 33: 22.756 distance: 28 - 29: 16.409 distance: 28 - 31: 20.769 distance: 29 - 30: 14.085 distance: 29 - 34: 5.081 distance: 31 - 32: 17.029 distance: 32 - 33: 5.162 distance: 34 - 35: 10.822 distance: 35 - 36: 14.874 distance: 36 - 37: 18.675 distance: 36 - 44: 14.558 distance: 38 - 39: 25.229 distance: 39 - 40: 18.929 distance: 39 - 41: 15.221 distance: 40 - 42: 15.797 distance: 41 - 43: 18.696 distance: 42 - 43: 7.951 distance: 44 - 45: 9.459 distance: 44 - 50: 5.305 distance: 45 - 46: 15.646 distance: 45 - 48: 11.789 distance: 46 - 47: 8.253 distance: 46 - 51: 3.878 distance: 48 - 49: 6.974 distance: 49 - 50: 12.211 distance: 51 - 52: 4.981 distance: 52 - 53: 5.887 distance: 52 - 55: 9.948 distance: 53 - 54: 3.043 distance: 53 - 60: 3.870 distance: 55 - 56: 6.459 distance: 56 - 57: 8.742 distance: 57 - 58: 5.303 distance: 58 - 59: 13.163 distance: 60 - 61: 4.114 distance: 60 - 66: 8.610 distance: 61 - 62: 4.829 distance: 61 - 64: 3.364 distance: 62 - 63: 8.000 distance: 62 - 67: 3.108 distance: 64 - 65: 10.043 distance: 65 - 66: 3.605 distance: 68 - 69: 4.334 distance: 68 - 71: 5.547 distance: 69 - 70: 4.474 distance: 69 - 76: 3.453 distance: 71 - 72: 7.584 distance: 72 - 73: 9.278 distance: 73 - 74: 5.163 distance: 74 - 75: 14.035 distance: 76 - 77: 6.460 distance: 77 - 78: 8.297 distance: 77 - 80: 4.376 distance: 78 - 79: 6.414 distance: 80 - 81: 4.213 distance: 81 - 82: 9.274 distance: 82 - 83: 11.131 distance: 82 - 84: 10.954 distance: 86 - 87: 4.724 distance: 86 - 89: 5.371 distance: 87 - 88: 9.686 distance: 89 - 90: 7.012 distance: 90 - 91: 3.848 distance: 90 - 92: 7.536 distance: 91 - 93: 4.715 distance: 92 - 94: 4.578 distance: 93 - 95: 6.557 distance: 96 - 97: 8.881 distance: 97 - 98: 8.866 distance: 97 - 100: 15.850 distance: 98 - 99: 16.086 distance: 98 - 102: 5.645 distance: 100 - 101: 15.974 distance: 102 - 103: 4.137 distance: 103 - 104: 5.403 distance: 103 - 106: 13.830 distance: 104 - 105: 10.081 distance: 106 - 107: 14.464