Starting phenix.real_space_refine on Wed Feb 21 16:58:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/02_2024/7z9k_14573_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/02_2024/7z9k_14573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/02_2024/7z9k_14573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/02_2024/7z9k_14573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/02_2024/7z9k_14573_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/02_2024/7z9k_14573_trim_updated.pdb" } resolution = 3.25 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= 0.002 sd= 0.025 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: 7 Type Number sf(0) Gaussians P 64 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 9821 2.51 5 N 2840 2.21 5 O 3171 1.98 5 H 15359 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31315 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8207 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "C" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8207 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 450 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 448 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 561 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IL1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.77, per 1000 atoms: 0.47 Number of scatterers: 31315 At special positions: 0 Unit cell: (128.14, 138.46, 135.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 64 15.00 Mg 2 11.99 O 3171 8.00 N 2840 7.00 C 9821 6.00 H 15359 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.54 Conformation dependent library (CDL) restraints added in 3.0 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 22 sheets defined 43.5% alpha, 9.1% beta 9 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 16.25 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.514A pdb=" N MET A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.596A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 227 through 235 removed outlier: 3.570A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.526A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.739A pdb=" N ALA A 421 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 422 " --> pdb=" O ASN A 419 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A 423 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 418 through 424' Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 468 through 493 removed outlier: 3.590A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 513 Processing helix chain 'B' and resid 427 through 435 Processing helix chain 'B' and resid 458 through 463 removed outlier: 3.733A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 458 through 463' Processing helix chain 'B' and resid 465 through 474 Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 578 through 596 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 626 through 638 removed outlier: 3.799A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 683 Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.978A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 730 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 771 through 781 Processing helix chain 'B' and resid 785 through 794 Processing helix chain 'B' and resid 797 through 800 No H-bonds generated for 'chain 'B' and resid 797 through 800' Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 43 through 54 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.636A pdb=" N ALA C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 205 through 210 Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 313 through 323 removed outlier: 3.709A pdb=" N TYR C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 399 removed outlier: 3.535A pdb=" N ILE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 3.960A pdb=" N HIS C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.999A pdb=" N ALA C 422 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 463 through 466 Processing helix chain 'C' and resid 468 through 492 removed outlier: 3.558A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 513 Processing helix chain 'D' and resid 426 through 434 removed outlier: 3.647A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 466 through 474 Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 519 through 524 Processing helix chain 'D' and resid 550 through 560 Processing helix chain 'D' and resid 578 through 597 removed outlier: 3.585A pdb=" N ARG D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET D 597 " --> pdb=" O MET D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 610 removed outlier: 3.990A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 639 Processing helix chain 'D' and resid 679 through 683 Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.721A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 730 Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 747 through 753 Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 785 through 794 Processing sheet with id= A, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 171 through 174 Processing sheet with id= D, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.676A pdb=" N GLU A 520 " --> pdb=" O ILE A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 237 through 243 Processing sheet with id= F, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.746A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= H, first strand: chain 'B' and resid 419 through 421 removed outlier: 6.997A pdb=" N SER B 492 " --> pdb=" O LEU B 420 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 528 through 530 Processing sheet with id= J, first strand: chain 'B' and resid 542 through 546 removed outlier: 4.088A pdb=" N GLN B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 646 through 648 Processing sheet with id= L, first strand: chain 'B' and resid 651 through 653 Processing sheet with id= M, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= N, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= O, first strand: chain 'C' and resid 171 through 174 Processing sheet with id= P, first strand: chain 'C' and resid 520 through 522 removed outlier: 3.902A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 246 through 249 Processing sheet with id= R, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= S, first strand: chain 'D' and resid 419 through 421 removed outlier: 6.882A pdb=" N SER D 492 " --> pdb=" O LEU D 420 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 528 through 530 Processing sheet with id= U, first strand: chain 'D' and resid 543 through 546 Processing sheet with id= V, first strand: chain 'D' and resid 646 through 652 593 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 12.18 Time building geometry restraints manager: 25.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15351 1.03 - 1.23: 31 1.23 - 1.42: 6710 1.42 - 1.61: 9511 1.61 - 1.81: 109 Bond restraints: 31712 Sorted by residual: bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.612 0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" OH PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.769 1.612 0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" C7 IL1 A 901 " pdb=" O3 IL1 A 901 " ideal model delta sigma weight residual 1.247 1.306 -0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" O1P PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.522 1.479 0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" O2P PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.518 1.479 0.039 2.00e-02 2.50e+03 3.81e+00 ... (remaining 31707 not shown) Histogram of bond angle deviations from ideal: 100.37 - 115.98: 41241 115.98 - 131.59: 16166 131.59 - 147.21: 34 147.21 - 162.82: 0 162.82 - 178.43: 1 Bond angle restraints: 57442 Sorted by residual: angle pdb=" OH PTR A 122 " pdb=" P PTR A 122 " pdb=" O2P PTR A 122 " ideal model delta sigma weight residual 99.92 109.59 -9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" O3' DA F 7 " pdb=" C3' DA F 7 " pdb=" C2' DA F 7 " ideal model delta sigma weight residual 111.50 116.29 -4.79 1.50e+00 4.44e-01 1.02e+01 angle pdb=" O3' DG E 7 " pdb=" C3' DG E 7 " pdb=" C2' DG E 7 " ideal model delta sigma weight residual 111.50 116.19 -4.69 1.50e+00 4.44e-01 9.76e+00 angle pdb=" OH PTR C 122 " pdb=" P PTR C 122 " pdb=" O2P PTR C 122 " ideal model delta sigma weight residual 99.92 108.52 -8.60 3.00e+00 1.11e-01 8.22e+00 angle pdb=" C3' DA F 7 " pdb=" O3' DA F 7 " pdb=" P DG F 8 " ideal model delta sigma weight residual 120.20 124.22 -4.02 1.50e+00 4.44e-01 7.19e+00 ... (remaining 57437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.29: 13785 25.29 - 50.58: 550 50.58 - 75.86: 150 75.86 - 101.15: 1 101.15 - 126.44: 2 Dihedral angle restraints: 14488 sinusoidal: 8514 harmonic: 5974 Sorted by residual: dihedral pdb=" CA ARG A 32 " pdb=" C ARG A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta harmonic sigma weight residual -180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ARG C 32 " pdb=" C ARG C 32 " pdb=" N ALA C 33 " pdb=" CA ALA C 33 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLY D 577 " pdb=" C GLY D 577 " pdb=" N GLU D 578 " pdb=" CA GLU D 578 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1696 0.033 - 0.066: 574 0.066 - 0.100: 135 0.100 - 0.133: 88 0.133 - 0.166: 10 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 2500 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 IL1 A 901 " -0.076 2.00e-02 2.50e+03 4.42e-02 3.90e+01 pdb=" C14 IL1 A 901 " 0.018 2.00e-02 2.50e+03 pdb=" C15 IL1 A 901 " 0.030 2.00e-02 2.50e+03 pdb=" C16 IL1 A 901 " 0.028 2.00e-02 2.50e+03 pdb=" C17 IL1 A 901 " 0.017 2.00e-02 2.50e+03 pdb=" C37 IL1 A 901 " 0.030 2.00e-02 2.50e+03 pdb=" N10 IL1 A 901 " 0.029 2.00e-02 2.50e+03 pdb=" N2 IL1 A 901 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C IL1 A 901 " 0.022 2.00e-02 2.50e+03 3.72e-02 3.46e+01 pdb=" O IL1 A 901 " 0.031 2.00e-02 2.50e+03 pdb=" C1 IL1 A 901 " 0.007 2.00e-02 2.50e+03 pdb=" C10 IL1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C11 IL1 A 901 " 0.033 2.00e-02 2.50e+03 pdb=" C12 IL1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C2 IL1 A 901 " -0.075 2.00e-02 2.50e+03 pdb=" C38 IL1 A 901 " 0.023 2.00e-02 2.50e+03 pdb=" N1 IL1 A 901 " -0.059 2.00e-02 2.50e+03 pdb=" O8 IL1 A 901 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 IL1 A 901 " -0.069 2.00e-02 2.50e+03 3.15e-02 2.23e+01 pdb=" C29 IL1 A 901 " 0.017 2.00e-02 2.50e+03 pdb=" C30 IL1 A 901 " 0.024 2.00e-02 2.50e+03 pdb=" C31 IL1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C32 IL1 A 901 " 0.014 2.00e-02 2.50e+03 pdb=" C33 IL1 A 901 " -0.015 2.00e-02 2.50e+03 pdb=" C34 IL1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C35 IL1 A 901 " 0.024 2.00e-02 2.50e+03 pdb=" N8 IL1 A 901 " -0.037 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 4917 2.30 - 2.88: 69725 2.88 - 3.45: 71672 3.45 - 4.03: 99848 4.03 - 4.60: 155676 Nonbonded interactions: 401838 Sorted by model distance: nonbonded pdb="HD21 ASN D 569 " pdb=" O LEU D 700 " model vdw 1.725 1.850 nonbonded pdb=" O GLN D 749 " pdb=" HG1 THR D 753 " model vdw 1.730 1.850 nonbonded pdb=" OD1 ASP D 498 " pdb=" H ALA D 499 " model vdw 1.739 1.850 nonbonded pdb=" OE2 GLU D 424 " pdb="HO3' DA F 14 " model vdw 1.742 1.850 nonbonded pdb=" O GLN D 612 " pdb="HH12 ARG D 698 " model vdw 1.749 1.850 ... (remaining 401833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 524) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 3.450 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: 0.480 Extract box with map and model: 14.970 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 108.440 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.004 0.157 16353 Z= 0.249 Angle : 0.590 9.667 22381 Z= 0.315 Chirality : 0.040 0.166 2503 Planarity : 0.004 0.048 2710 Dihedral : 12.991 126.440 6420 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.13 % Allowed : 2.26 % Favored : 97.61 % 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: 0.91 (0.20), residues: 1824 helix: 2.61 (0.18), residues: 841 sheet: 0.00 (0.41), residues: 169 loop : -1.54 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 647 HIS 0.003 0.001 HIS A 339 PHE 0.007 0.001 PHE C 96 TYR 0.010 0.001 TYR C 266 ARG 0.002 0.000 ARG B 689 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 LYS cc_start: 0.6868 (mmtp) cc_final: 0.6644 (mtmt) REVERT: B 552 MET cc_start: 0.8346 (tpt) cc_final: 0.7857 (tpt) REVERT: B 598 GLU cc_start: 0.7858 (tt0) cc_final: 0.7649 (tt0) REVERT: C 258 THR cc_start: 0.8920 (p) cc_final: 0.8607 (p) REVERT: C 402 THR cc_start: 0.7311 (p) cc_final: 0.6534 (p) REVERT: D 415 PRO cc_start: 0.8236 (Cg_endo) cc_final: 0.7929 (Cg_exo) outliers start: 2 outliers final: 0 residues processed: 291 average time/residue: 0.8518 time to fit residues: 334.1583 Evaluate side-chains 148 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 GLN B 531 GLN B 567 HIS ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 746 ASN D 749 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16353 Z= 0.223 Angle : 0.497 6.092 22381 Z= 0.275 Chirality : 0.040 0.247 2503 Planarity : 0.004 0.050 2710 Dihedral : 15.359 132.948 2768 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.77 % Allowed : 6.32 % Favored : 92.90 % 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: 1.03 (0.20), residues: 1824 helix: 2.76 (0.18), residues: 842 sheet: 0.08 (0.41), residues: 166 loop : -1.55 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.004 0.001 HIS A 262 PHE 0.015 0.001 PHE D 719 TYR 0.010 0.001 TYR A 266 ARG 0.004 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 552 MET cc_start: 0.8419 (tpt) cc_final: 0.7790 (tpt) REVERT: B 608 GLU cc_start: 0.5529 (mm-30) cc_final: 0.5100 (mm-30) REVERT: D 415 PRO cc_start: 0.8436 (Cg_endo) cc_final: 0.8065 (Cg_exo) REVERT: D 758 GLU cc_start: 0.6720 (tp30) cc_final: 0.6504 (tp30) outliers start: 12 outliers final: 9 residues processed: 152 average time/residue: 0.7031 time to fit residues: 158.4922 Evaluate side-chains 140 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 292 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 169 optimal weight: 0.0010 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16353 Z= 0.193 Angle : 0.475 5.709 22381 Z= 0.263 Chirality : 0.039 0.214 2503 Planarity : 0.004 0.046 2710 Dihedral : 15.586 136.600 2768 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.90 % Allowed : 7.16 % Favored : 91.94 % 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: 1.05 (0.20), residues: 1824 helix: 2.80 (0.18), residues: 841 sheet: -0.11 (0.41), residues: 170 loop : -1.52 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.004 0.001 HIS A 262 PHE 0.012 0.001 PHE B 719 TYR 0.010 0.001 TYR C 266 ARG 0.003 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 552 MET cc_start: 0.8414 (tpt) cc_final: 0.7794 (tpt) REVERT: B 598 GLU cc_start: 0.7981 (tt0) cc_final: 0.7765 (mt-10) REVERT: B 608 GLU cc_start: 0.5517 (mm-30) cc_final: 0.5070 (mm-30) REVERT: C 516 LYS cc_start: 0.7766 (pttt) cc_final: 0.7499 (tttm) REVERT: D 758 GLU cc_start: 0.6924 (tp30) cc_final: 0.6588 (tp30) outliers start: 14 outliers final: 10 residues processed: 146 average time/residue: 0.6177 time to fit residues: 135.0176 Evaluate side-chains 136 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 491 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16353 Z= 0.253 Angle : 0.502 5.765 22381 Z= 0.279 Chirality : 0.040 0.222 2503 Planarity : 0.004 0.046 2710 Dihedral : 15.835 133.732 2768 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.29 % Allowed : 7.42 % Favored : 91.29 % 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: 0.88 (0.20), residues: 1824 helix: 2.70 (0.18), residues: 836 sheet: -0.01 (0.41), residues: 176 loop : -1.68 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.006 0.001 HIS A 262 PHE 0.010 0.001 PHE B 719 TYR 0.012 0.001 TYR C 266 ARG 0.004 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 516 LYS cc_start: 0.7848 (pttt) cc_final: 0.7577 (tttm) outliers start: 20 outliers final: 12 residues processed: 139 average time/residue: 0.6249 time to fit residues: 130.1298 Evaluate side-chains 132 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 491 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 0.2980 chunk 74 optimal weight: 9.9990 chunk 153 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16353 Z= 0.228 Angle : 0.490 5.788 22381 Z= 0.272 Chirality : 0.040 0.220 2503 Planarity : 0.004 0.046 2710 Dihedral : 15.963 136.079 2768 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.03 % Allowed : 7.42 % Favored : 91.55 % 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: 0.89 (0.20), residues: 1824 helix: 2.73 (0.18), residues: 827 sheet: -0.03 (0.41), residues: 176 loop : -1.65 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.005 0.001 HIS A 262 PHE 0.011 0.001 PHE B 719 TYR 0.010 0.001 TYR C 266 ARG 0.003 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 504 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: C 516 LYS cc_start: 0.7856 (pttt) cc_final: 0.7588 (tttm) REVERT: D 605 MET cc_start: 0.5413 (ttm) cc_final: 0.5109 (ttp) outliers start: 16 outliers final: 11 residues processed: 136 average time/residue: 0.6546 time to fit residues: 132.4984 Evaluate side-chains 132 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 491 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16353 Z= 0.251 Angle : 0.504 5.794 22381 Z= 0.280 Chirality : 0.040 0.223 2503 Planarity : 0.004 0.045 2710 Dihedral : 16.136 133.567 2768 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.29 % Allowed : 7.55 % Favored : 91.16 % 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: 0.77 (0.20), residues: 1824 helix: 2.64 (0.18), residues: 827 sheet: -0.11 (0.40), residues: 176 loop : -1.72 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.006 0.001 HIS A 262 PHE 0.009 0.001 PHE A 330 TYR 0.011 0.001 TYR C 266 ARG 0.004 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: C 516 LYS cc_start: 0.7890 (pttt) cc_final: 0.7636 (tttm) outliers start: 20 outliers final: 17 residues processed: 137 average time/residue: 0.6539 time to fit residues: 132.4184 Evaluate side-chains 139 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain D residue 491 HIS Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 671 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16353 Z= 0.159 Angle : 0.470 6.131 22381 Z= 0.261 Chirality : 0.039 0.222 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.108 135.888 2768 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.90 % Allowed : 8.26 % Favored : 90.84 % 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: 0.94 (0.20), residues: 1824 helix: 2.83 (0.18), residues: 826 sheet: -0.25 (0.40), residues: 170 loop : -1.61 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.016 0.001 HIS D 491 PHE 0.012 0.001 PHE B 719 TYR 0.011 0.001 TYR D 490 ARG 0.002 0.000 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 504 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: C 516 LYS cc_start: 0.7897 (pttt) cc_final: 0.7661 (tttm) outliers start: 14 outliers final: 13 residues processed: 135 average time/residue: 0.6466 time to fit residues: 128.7714 Evaluate side-chains 140 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16353 Z= 0.181 Angle : 0.466 5.780 22381 Z= 0.258 Chirality : 0.039 0.213 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.141 134.554 2768 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.03 % Allowed : 8.52 % Favored : 90.45 % 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: 0.96 (0.20), residues: 1824 helix: 2.86 (0.18), residues: 826 sheet: -0.29 (0.40), residues: 170 loop : -1.61 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.015 0.001 HIS D 491 PHE 0.008 0.001 PHE B 719 TYR 0.013 0.001 TYR D 490 ARG 0.002 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: C 504 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: C 516 LYS cc_start: 0.7831 (pttt) cc_final: 0.7589 (tttm) outliers start: 16 outliers final: 14 residues processed: 135 average time/residue: 0.6354 time to fit residues: 128.2439 Evaluate side-chains 139 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 671 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 GLN ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16353 Z= 0.370 Angle : 0.557 5.900 22381 Z= 0.311 Chirality : 0.043 0.229 2503 Planarity : 0.005 0.046 2710 Dihedral : 16.353 131.138 2768 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.16 % Allowed : 8.65 % Favored : 90.19 % 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: 0.47 (0.20), residues: 1824 helix: 2.41 (0.18), residues: 829 sheet: -0.25 (0.40), residues: 176 loop : -1.91 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 629 HIS 0.008 0.001 HIS A 262 PHE 0.013 0.001 PHE A 330 TYR 0.013 0.001 TYR C 266 ARG 0.006 0.001 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: C 504 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: C 516 LYS cc_start: 0.7896 (pttt) cc_final: 0.7679 (tttm) REVERT: D 663 ILE cc_start: 0.4233 (OUTLIER) cc_final: 0.3843 (tt) outliers start: 18 outliers final: 12 residues processed: 133 average time/residue: 0.6444 time to fit residues: 127.5739 Evaluate side-chains 130 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 663 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 90 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16353 Z= 0.141 Angle : 0.465 5.928 22381 Z= 0.259 Chirality : 0.039 0.209 2503 Planarity : 0.003 0.042 2710 Dihedral : 16.259 136.673 2768 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.84 % Allowed : 9.23 % Favored : 89.94 % 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: 0.83 (0.20), residues: 1824 helix: 2.74 (0.18), residues: 829 sheet: -0.38 (0.40), residues: 170 loop : -1.69 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 647 HIS 0.003 0.001 HIS A 262 PHE 0.010 0.001 PHE B 719 TYR 0.008 0.001 TYR C 266 ARG 0.002 0.000 ARG A 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 504 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: C 516 LYS cc_start: 0.7832 (pttt) cc_final: 0.7595 (tttm) REVERT: D 605 MET cc_start: 0.5127 (ttm) cc_final: 0.4736 (ttp) REVERT: D 663 ILE cc_start: 0.4193 (OUTLIER) cc_final: 0.3897 (tt) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.6157 time to fit residues: 118.5494 Evaluate side-chains 132 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 663 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.0270 chunk 147 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.143992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098274 restraints weight = 67979.793| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.38 r_work: 0.3042 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16353 Z= 0.185 Angle : 0.468 5.974 22381 Z= 0.260 Chirality : 0.039 0.212 2503 Planarity : 0.004 0.044 2710 Dihedral : 16.211 134.505 2768 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.84 % Allowed : 9.16 % Favored : 90.00 % 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: 0.85 (0.20), residues: 1824 helix: 2.76 (0.18), residues: 829 sheet: -0.35 (0.40), residues: 170 loop : -1.68 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.004 0.001 HIS A 262 PHE 0.010 0.001 PHE B 706 TYR 0.020 0.001 TYR B 687 ARG 0.002 0.000 ARG C 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6749.23 seconds wall clock time: 120 minutes 0.27 seconds (7200.27 seconds total)