Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 15 17:11:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/10_2023/7z9k_14573_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/10_2023/7z9k_14573.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/10_2023/7z9k_14573_trim_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/10_2023/7z9k_14573_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/10_2023/7z9k_14573_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/10_2023/7z9k_14573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/10_2023/7z9k_14573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/10_2023/7z9k_14573_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9k_14573/10_2023/7z9k_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 13.80, per 1000 atoms: 0.44 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: 27.01 Conformation dependent library (CDL) restraints added in 2.7 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: 14.77 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: 11.89 Time building geometry restraints manager: 27.68 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=" C23 IL1 A 901 " pdb=" N6 IL1 A 901 " ideal model delta sigma weight residual 1.473 1.340 0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" N IL1 A 901 " pdb=" C2 IL1 A 901 " ideal model delta sigma weight residual 1.489 1.357 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C18 IL1 A 901 " pdb=" N2 IL1 A 901 " ideal model delta sigma weight residual 1.487 1.356 0.131 2.00e-02 2.50e+03 4.27e+01 ... (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=" C12 IL1 A 901 " pdb=" C38 IL1 A 901 " pdb=" O8 IL1 A 901 " ideal model delta sigma weight residual 95.70 117.79 -22.09 3.00e+00 1.11e-01 5.42e+01 angle pdb=" C IL1 A 901 " pdb=" C38 IL1 A 901 " pdb=" O8 IL1 A 901 " ideal model delta sigma weight residual 143.57 122.01 21.56 3.00e+00 1.11e-01 5.17e+01 angle pdb=" C37 IL1 A 901 " pdb=" C17 IL1 A 901 " pdb=" N2 IL1 A 901 " ideal model delta sigma weight residual 107.96 124.62 -16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" C16 IL1 A 901 " pdb=" C17 IL1 A 901 " pdb=" N2 IL1 A 901 " ideal model delta sigma weight residual 131.92 118.05 13.87 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C11 IL1 A 901 " pdb=" C12 IL1 A 901 " pdb=" N1 IL1 A 901 " ideal model delta sigma weight residual 110.11 122.89 -12.78 3.00e+00 1.11e-01 1.82e+01 ... (remaining 57437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.29: 12016 25.29 - 50.58: 305 50.58 - 75.86: 69 75.86 - 101.15: 1 101.15 - 126.44: 2 Dihedral angle restraints: 12393 sinusoidal: 6419 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 12390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1876 0.040 - 0.080: 469 0.080 - 0.120: 115 0.120 - 0.159: 38 0.159 - 0.199: 5 Chirality restraints: 2503 Sorted by residual: chirality pdb=" C19 IL1 A 901 " pdb=" C18 IL1 A 901 " pdb=" C20 IL1 A 901 " pdb=" N6 IL1 A 901 " both_signs ideal model delta sigma weight residual False 2.63 2.43 0.20 2.00e-01 2.50e+01 9.93e-01 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 ... (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: 0.010 Normalize map: mean=0, sd=1: 3.820 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: 0.470 Extract box with map and model: 14.990 Check model and map are aligned: 0.460 Set scattering table: 0.310 Process input model: 108.280 Find NCS groups from input model: 1.280 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.660 ------------------------------------------------------------------------------- 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 : 0.005 0.157 16353 Z= 0.291 Angle : 0.673 22.087 22381 Z= 0.333 Chirality : 0.041 0.199 2503 Planarity : 0.004 0.048 2710 Dihedral : 12.656 126.440 6319 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 *********************** 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 : 2.431 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 outliers start: 2 outliers final: 0 residues processed: 291 average time/residue: 0.8373 time to fit residues: 327.7663 Evaluate side-chains 146 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1331 ------------------------------------------------------------------------------- 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: 10.0000 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 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: 0.8156 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16353 Z= 0.215 Angle : 0.515 8.417 22381 Z= 0.279 Chirality : 0.040 0.147 2503 Planarity : 0.004 0.049 2710 Dihedral : 15.131 133.114 2667 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.77 % Allowed : 6.58 % Favored : 92.65 % 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: 1.02 (0.20), residues: 1824 helix: 2.77 (0.18), residues: 842 sheet: 0.06 (0.41), residues: 166 loop : -1.56 (0.20), residues: 816 *********************** 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 152 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 2.425 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 outliers start: 12 outliers final: 9 residues processed: 147 average time/residue: 0.7083 time to fit residues: 153.3953 Evaluate side-chains 136 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3670 time to fit residues: 8.9953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 135 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8170 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16353 Z= 0.190 Angle : 0.491 8.983 22381 Z= 0.266 Chirality : 0.039 0.145 2503 Planarity : 0.003 0.042 2710 Dihedral : 15.372 136.100 2667 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.45 % Allowed : 7.68 % Favored : 91.87 % 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: 2.80 (0.18), residues: 840 sheet: 0.04 (0.41), residues: 166 loop : -1.57 (0.20), residues: 818 *********************** 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 138 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 2.348 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 outliers start: 7 outliers final: 4 residues processed: 137 average time/residue: 0.6300 time to fit residues: 128.5318 Evaluate side-chains 128 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 2.470 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3602 time to fit residues: 5.8311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 48 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 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16353 Z= 0.365 Angle : 0.581 8.072 22381 Z= 0.320 Chirality : 0.043 0.168 2503 Planarity : 0.004 0.049 2710 Dihedral : 15.762 132.085 2667 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.03 % Allowed : 7.48 % Favored : 91.48 % 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: 0.54 (0.20), residues: 1824 helix: 2.39 (0.18), residues: 835 sheet: -0.06 (0.41), residues: 176 loop : -1.86 (0.19), residues: 813 *********************** 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: 16 poor density : 129 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 142 average time/residue: 0.6515 time to fit residues: 137.2527 Evaluate side-chains 127 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 2.619 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3600 time to fit residues: 7.8119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** C 319 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: 0.8275 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16353 Z= 0.297 Angle : 0.539 9.256 22381 Z= 0.296 Chirality : 0.041 0.159 2503 Planarity : 0.004 0.042 2710 Dihedral : 15.928 135.418 2667 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.84 % Allowed : 8.19 % Favored : 90.97 % 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: 0.49 (0.20), residues: 1824 helix: 2.39 (0.18), residues: 827 sheet: -0.17 (0.40), residues: 176 loop : -1.87 (0.19), residues: 821 *********************** 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 137 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 2.523 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 outliers start: 13 outliers final: 9 residues processed: 136 average time/residue: 0.6414 time to fit residues: 130.3905 Evaluate side-chains 126 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 2.413 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3592 time to fit residues: 8.9433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16353 Z= 0.177 Angle : 0.490 9.214 22381 Z= 0.268 Chirality : 0.039 0.147 2503 Planarity : 0.003 0.041 2710 Dihedral : 15.923 136.134 2667 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.32 % Allowed : 8.90 % Favored : 90.77 % 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: 0.71 (0.20), residues: 1824 helix: 2.63 (0.18), residues: 825 sheet: -0.38 (0.40), residues: 170 loop : -1.72 (0.19), residues: 829 *********************** 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 126 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 124 average time/residue: 0.6611 time to fit residues: 122.5990 Evaluate side-chains 117 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 2.475 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3795 time to fit residues: 4.6383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- 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: 0.8235 moved from start: 0.3330 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= 0.186 Angle : 0.489 9.179 22381 Z= 0.266 Chirality : 0.039 0.147 2503 Planarity : 0.003 0.041 2710 Dihedral : 15.953 134.974 2667 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.39 % Allowed : 9.10 % Favored : 90.52 % 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 (0.20), residues: 1824 helix: 2.69 (0.18), residues: 826 sheet: -0.40 (0.40), residues: 170 loop : -1.66 (0.19), residues: 828 *********************** 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 126 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 2.557 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 outliers start: 6 outliers final: 3 residues processed: 125 average time/residue: 0.6564 time to fit residues: 122.3354 Evaluate side-chains 122 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 2.589 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3294 time to fit residues: 5.0308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.0570 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** 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: 0.8202 moved from start: 0.3345 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= 0.145 Angle : 0.467 8.694 22381 Z= 0.253 Chirality : 0.038 0.142 2503 Planarity : 0.003 0.039 2710 Dihedral : 15.992 135.756 2667 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.26 % Allowed : 9.03 % Favored : 90.71 % 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: 2.81 (0.18), residues: 828 sheet: -0.37 (0.39), residues: 170 loop : -1.55 (0.20), residues: 826 *********************** 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 135 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 134 average time/residue: 0.6424 time to fit residues: 127.4605 Evaluate side-chains 128 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 2.317 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3426 time to fit residues: 4.7545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.8249 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16353 Z= 0.227 Angle : 0.500 8.970 22381 Z= 0.272 Chirality : 0.040 0.148 2503 Planarity : 0.003 0.040 2710 Dihedral : 16.008 133.066 2667 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.32 % Allowed : 8.97 % Favored : 90.71 % 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: 2.72 (0.18), residues: 826 sheet: -0.25 (0.40), residues: 176 loop : -1.68 (0.19), residues: 822 *********************** 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 127 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 124 average time/residue: 0.6628 time to fit residues: 121.4882 Evaluate side-chains 119 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 2.398 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3578 time to fit residues: 4.3504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8227 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16353 Z= 0.173 Angle : 0.482 9.012 22381 Z= 0.262 Chirality : 0.039 0.142 2503 Planarity : 0.003 0.039 2710 Dihedral : 16.048 134.891 2667 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.19 % Allowed : 9.29 % Favored : 90.52 % 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 (0.20), residues: 1824 helix: 2.73 (0.18), residues: 828 sheet: -0.43 (0.39), residues: 170 loop : -1.61 (0.20), residues: 826 ********************** 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 124 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 2.461 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 outliers start: 3 outliers final: 3 residues processed: 121 average time/residue: 0.6394 time to fit residues: 116.2797 Evaluate side-chains 120 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 2.653 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3575 time to fit residues: 5.2325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 41 optimal weight: 6.9990 chunk 147 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3902 r_free = 0.3902 target = 0.145944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100810 restraints weight = 67830.468| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.26 r_work: 0.3092 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3529 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= 0.138 Angle : 0.462 8.354 22381 Z= 0.251 Chirality : 0.038 0.144 2503 Planarity : 0.003 0.039 2710 Dihedral : 16.040 135.728 2667 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % 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: 2.91 (0.18), residues: 826 sheet: -0.38 (0.39), residues: 170 loop : -1.50 (0.20), residues: 828 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6458.07 seconds wall clock time: 115 minutes 6.21 seconds (6906.21 seconds total)