Starting phenix.real_space_refine on Thu Mar 14 18:38:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aap_11692/03_2024/7aap_11692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aap_11692/03_2024/7aap_11692.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aap_11692/03_2024/7aap_11692_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aap_11692/03_2024/7aap_11692_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aap_11692/03_2024/7aap_11692_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aap_11692/03_2024/7aap_11692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aap_11692/03_2024/7aap_11692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aap_11692/03_2024/7aap_11692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aap_11692/03_2024/7aap_11692_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 26 5.49 5 Mg 3 5.21 5 S 66 5.16 5 C 5919 2.51 5 N 1581 2.21 5 O 1848 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "D ARG 96": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9446 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 7345 Classifications: {'peptide': 911} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 880} Chain breaks: 1 Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 513 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Chain: "D" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "P" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' MG': 2, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GE6': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 42.374 62.670 43.895 1.00 49.57 S ATOM 2487 SG CYS A 306 42.428 61.687 40.192 1.00 46.12 S ATOM 2519 SG CYS A 310 45.719 61.837 42.215 1.00 41.58 S ATOM 3927 SG CYS A 487 24.274 58.627 52.787 1.00 52.25 S ATOM 5180 SG CYS A 645 23.549 58.149 49.031 1.00 57.21 S ATOM 5186 SG CYS A 646 26.332 60.537 50.194 1.00 55.39 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O POP A1005 " occ=0.50 ... (7 atoms not shown) pdb=" P2 POP A1005 " occ=0.50 Time building chain proxies: 4.60, per 1000 atoms: 0.49 Number of scatterers: 9446 At special positions: 0 Unit cell: (102.7, 92.95, 117.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 26 15.00 Mg 3 11.99 F 1 9.00 O 1848 8.00 N 1581 7.00 C 5919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " Number of angles added : 6 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 8 sheets defined 46.6% alpha, 10.5% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.613A pdb=" N THR A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.829A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 198 removed outlier: 4.478A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 3.969A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.301A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.656A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.734A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.783A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.878A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.557A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 580 removed outlier: 3.538A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.653A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.541A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 852 through 871 removed outlier: 3.515A pdb=" N ILE A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.657A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 893 removed outlier: 3.813A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 removed outlier: 3.760A pdb=" N TYR A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 915' Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.631A pdb=" N VAL B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.567A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 4.073A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.703A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 18 removed outlier: 3.841A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.545A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 40 " --> pdb=" O HIS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 4.090A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'D' and resid 85 through 98 removed outlier: 3.555A pdb=" N THR D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 110 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.963A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 removed outlier: 3.750A pdb=" N VAL A 31 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 33 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 99 through 103 Processing sheet with id= D, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.530A pdb=" N VAL A 335 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 555 through 559 removed outlier: 4.505A pdb=" N ARG A 555 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.110A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.611A pdb=" N MET A 818 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.571A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2844 1.34 - 1.45: 1619 1.45 - 1.57: 5083 1.57 - 1.69: 47 1.69 - 1.81: 99 Bond restraints: 9692 Sorted by residual: bond pdb=" C02 GE6 T1601 " pdb=" C03 GE6 T1601 " ideal model delta sigma weight residual 1.263 1.531 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C03 GE6 T1601 " pdb=" O01 GE6 T1601 " ideal model delta sigma weight residual 1.655 1.417 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C01 GE6 T1601 " pdb=" C04 GE6 T1601 " ideal model delta sigma weight residual 1.350 1.530 -0.180 2.00e-02 2.50e+03 8.07e+01 bond pdb=" C01 GE6 T1601 " pdb=" C02 GE6 T1601 " ideal model delta sigma weight residual 1.675 1.527 0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" C06 GE6 T1601 " pdb=" C07 GE6 T1601 " ideal model delta sigma weight residual 1.521 1.375 0.146 2.00e-02 2.50e+03 5.34e+01 ... (remaining 9687 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.41: 239 105.41 - 112.57: 4997 112.57 - 119.73: 3135 119.73 - 126.89: 4736 126.89 - 134.05: 143 Bond angle restraints: 13250 Sorted by residual: angle pdb=" N ASN A 552 " pdb=" CA ASN A 552 " pdb=" C ASN A 552 " ideal model delta sigma weight residual 113.20 109.15 4.05 1.21e+00 6.83e-01 1.12e+01 angle pdb=" O13 GE6 T1601 " pdb=" P02 GE6 T1601 " pdb=" O14 GE6 T1601 " ideal model delta sigma weight residual 109.44 119.14 -9.70 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CA GLU A 917 " pdb=" CB GLU A 917 " pdb=" CG GLU A 917 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 angle pdb=" O07 GE6 T1601 " pdb=" P02 GE6 T1601 " pdb=" O10 GE6 T1601 " ideal model delta sigma weight residual 109.45 99.88 9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" O08 GE6 T1601 " pdb=" P01 GE6 T1601 " pdb=" O09 GE6 T1601 " ideal model delta sigma weight residual 109.47 118.68 -9.21 3.00e+00 1.11e-01 9.43e+00 ... (remaining 13245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.52: 5508 25.52 - 51.04: 214 51.04 - 76.56: 34 76.56 - 102.09: 7 102.09 - 127.61: 1 Dihedral angle restraints: 5764 sinusoidal: 2443 harmonic: 3321 Sorted by residual: dihedral pdb=" O4 POP A1005 " pdb=" O POP A1005 " pdb=" P2 POP A1005 " pdb=" P1 POP A1005 " ideal model delta sinusoidal sigma weight residual -57.41 70.19 -127.61 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" O2 POP A1005 " pdb=" O POP A1005 " pdb=" P1 POP A1005 " pdb=" P2 POP A1005 " ideal model delta sinusoidal sigma weight residual -88.77 -176.80 88.04 1 2.00e+01 2.50e-03 2.32e+01 dihedral pdb=" CA GLU A 917 " pdb=" C GLU A 917 " pdb=" N PRO A 918 " pdb=" CA PRO A 918 " ideal model delta harmonic sigma weight residual -180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 5761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1375 0.071 - 0.141: 117 0.141 - 0.212: 8 0.212 - 0.282: 0 0.282 - 0.353: 1 Chirality restraints: 1501 Sorted by residual: chirality pdb=" C02 GE6 T1601 " pdb=" C01 GE6 T1601 " pdb=" C03 GE6 T1601 " pdb=" O02 GE6 T1601 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C3' A T 18 " pdb=" C4' A T 18 " pdb=" O3' A T 18 " pdb=" C2' A T 18 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" C2' U P 20 " pdb=" C3' U P 20 " pdb=" O2' U P 20 " pdb=" C1' U P 20 " both_signs ideal model delta sigma weight residual False -2.75 -2.57 -0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 1498 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " 0.035 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO A 927 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A P 19 " -0.021 2.00e-02 2.50e+03 9.33e-03 2.39e+00 pdb=" N9 A P 19 " 0.005 2.00e-02 2.50e+03 pdb=" C8 A P 19 " 0.013 2.00e-02 2.50e+03 pdb=" N7 A P 19 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A P 19 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A P 19 " -0.010 2.00e-02 2.50e+03 pdb=" N6 A P 19 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A P 19 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A P 19 " 0.008 2.00e-02 2.50e+03 pdb=" N3 A P 19 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A P 19 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 50 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" CD GLU C 50 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU C 50 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 50 " 0.009 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 121 2.66 - 3.22: 8814 3.22 - 3.78: 14806 3.78 - 4.34: 21820 4.34 - 4.90: 33713 Nonbonded interactions: 79274 Sorted by model distance: nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1004 " model vdw 2.097 2.170 nonbonded pdb="MG MG A1004 " pdb=" O3 POP A1005 " model vdw 2.159 2.170 nonbonded pdb="MG MG A1004 " pdb=" O5 POP A1005 " model vdw 2.216 2.170 nonbonded pdb=" OG1 THR A 120 " pdb=" OD1 ASP A 211 " model vdw 2.225 2.440 nonbonded pdb=" OG SER B 173 " pdb=" OD1 ASP B 175 " model vdw 2.250 2.440 ... (remaining 79269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.860 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 30.720 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 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 : 0.006 0.268 9692 Z= 0.395 Angle : 0.528 9.698 13250 Z= 0.276 Chirality : 0.041 0.353 1501 Planarity : 0.002 0.054 1614 Dihedral : 13.522 127.608 3618 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.20 % Allowed : 0.10 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.59 (0.25), residues: 1110 helix: 0.54 (0.23), residues: 504 sheet: 0.89 (0.48), residues: 112 loop : 0.31 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.007 0.001 PHE A 741 TYR 0.014 0.001 TYR A 80 ARG 0.003 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 82 HIS cc_start: 0.8674 (t70) cc_final: 0.8472 (t-90) REVERT: A 98 LYS cc_start: 0.8405 (tttt) cc_final: 0.8101 (tttm) REVERT: A 196 MET cc_start: 0.8759 (mtp) cc_final: 0.8448 (mtp) REVERT: A 806 THR cc_start: 0.8299 (p) cc_final: 0.7425 (p) REVERT: A 855 MET cc_start: 0.7963 (mtm) cc_final: 0.7677 (mtt) REVERT: A 875 GLN cc_start: 0.8955 (tp40) cc_final: 0.8628 (tp40) REVERT: C 28 LEU cc_start: 0.8239 (mm) cc_final: 0.7726 (mt) REVERT: D 94 MET cc_start: 0.6740 (mtt) cc_final: 0.6086 (mpt) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 1.1211 time to fit residues: 210.7076 Evaluate side-chains 124 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 0.0470 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 416 ASN A 713 ASN B 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9692 Z= 0.226 Angle : 0.506 6.030 13250 Z= 0.274 Chirality : 0.041 0.157 1501 Planarity : 0.004 0.039 1614 Dihedral : 9.762 89.733 1534 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.02 % Allowed : 8.17 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.64 (0.25), residues: 1110 helix: 0.74 (0.23), residues: 510 sheet: 0.31 (0.45), residues: 132 loop : 0.31 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.019 0.001 PHE A 652 TYR 0.013 0.001 TYR B 135 ARG 0.007 0.001 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 82 HIS cc_start: 0.8410 (t70) cc_final: 0.8210 (t-90) REVERT: A 98 LYS cc_start: 0.8399 (tttt) cc_final: 0.8131 (tttm) REVERT: A 196 MET cc_start: 0.8949 (mtp) cc_final: 0.8611 (mtp) REVERT: A 855 MET cc_start: 0.7850 (mtm) cc_final: 0.7511 (mtt) REVERT: A 889 ARG cc_start: 0.7868 (mpt-90) cc_final: 0.7401 (mpt-90) REVERT: B 100 ASN cc_start: 0.7478 (p0) cc_final: 0.7071 (m-40) REVERT: B 163 ASP cc_start: 0.8274 (m-30) cc_final: 0.8010 (m-30) REVERT: C 26 SER cc_start: 0.8017 (t) cc_final: 0.7677 (p) REVERT: C 28 LEU cc_start: 0.8310 (mm) cc_final: 0.8104 (mt) REVERT: D 94 MET cc_start: 0.6759 (mtt) cc_final: 0.6164 (mpt) outliers start: 20 outliers final: 7 residues processed: 144 average time/residue: 1.1296 time to fit residues: 175.5217 Evaluate side-chains 127 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 892 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9692 Z= 0.299 Angle : 0.516 6.355 13250 Z= 0.280 Chirality : 0.042 0.155 1501 Planarity : 0.004 0.044 1614 Dihedral : 9.518 73.675 1534 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.42 % Allowed : 10.49 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.25), residues: 1110 helix: 0.69 (0.23), residues: 507 sheet: 0.06 (0.44), residues: 133 loop : 0.20 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.021 0.002 PHE A 652 TYR 0.014 0.002 TYR A 867 ARG 0.007 0.001 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8335 (t) cc_final: 0.8013 (p) REVERT: A 82 HIS cc_start: 0.8426 (t70) cc_final: 0.8194 (t-90) REVERT: A 98 LYS cc_start: 0.8358 (tttt) cc_final: 0.8114 (tttm) REVERT: A 404 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7934 (p0) REVERT: A 855 MET cc_start: 0.7853 (mtm) cc_final: 0.7459 (mtt) REVERT: B 100 ASN cc_start: 0.7378 (p0) cc_final: 0.7137 (m-40) REVERT: B 163 ASP cc_start: 0.8296 (m-30) cc_final: 0.8034 (m-30) REVERT: C 26 SER cc_start: 0.8104 (t) cc_final: 0.7834 (p) REVERT: D 94 MET cc_start: 0.6718 (mtt) cc_final: 0.6166 (mpt) outliers start: 24 outliers final: 11 residues processed: 137 average time/residue: 1.0681 time to fit residues: 158.0378 Evaluate side-chains 137 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 60 optimal weight: 0.0170 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9692 Z= 0.153 Angle : 0.453 6.124 13250 Z= 0.245 Chirality : 0.039 0.146 1501 Planarity : 0.003 0.028 1614 Dihedral : 9.017 73.431 1534 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.51 % Allowed : 13.22 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.50 (0.25), residues: 1110 helix: 0.65 (0.23), residues: 520 sheet: 0.28 (0.45), residues: 122 loop : 0.16 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 182 HIS 0.004 0.001 HIS A 613 PHE 0.017 0.001 PHE A 652 TYR 0.011 0.001 TYR A 788 ARG 0.010 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.963 Fit side-chains REVERT: A 42 VAL cc_start: 0.8197 (t) cc_final: 0.7892 (p) REVERT: A 82 HIS cc_start: 0.8366 (t70) cc_final: 0.8088 (t70) REVERT: A 98 LYS cc_start: 0.8341 (tttt) cc_final: 0.8098 (tttm) REVERT: A 855 MET cc_start: 0.7846 (mtm) cc_final: 0.7509 (ttm) REVERT: B 100 ASN cc_start: 0.7402 (p0) cc_final: 0.7172 (m-40) REVERT: B 163 ASP cc_start: 0.8282 (m-30) cc_final: 0.7686 (m-30) REVERT: C 26 SER cc_start: 0.8004 (t) cc_final: 0.7770 (p) REVERT: C 27 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7937 (mmtt) REVERT: D 94 MET cc_start: 0.6675 (mtt) cc_final: 0.6120 (mpt) outliers start: 15 outliers final: 8 residues processed: 131 average time/residue: 1.0218 time to fit residues: 145.1661 Evaluate side-chains 127 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B 108 ASN B 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9692 Z= 0.408 Angle : 0.559 9.656 13250 Z= 0.301 Chirality : 0.045 0.158 1501 Planarity : 0.004 0.029 1614 Dihedral : 9.075 73.955 1534 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.42 % Allowed : 13.42 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.44 (0.25), residues: 1110 helix: 0.62 (0.22), residues: 513 sheet: 0.17 (0.46), residues: 123 loop : 0.15 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 182 HIS 0.005 0.001 HIS A 892 PHE 0.024 0.002 PHE A 652 TYR 0.015 0.002 TYR A 867 ARG 0.006 0.001 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.958 Fit side-chains REVERT: A 42 VAL cc_start: 0.8504 (t) cc_final: 0.8192 (p) REVERT: A 98 LYS cc_start: 0.8386 (tttt) cc_final: 0.8161 (tttm) REVERT: A 855 MET cc_start: 0.7923 (mtm) cc_final: 0.7547 (ttm) REVERT: B 100 ASN cc_start: 0.7464 (p0) cc_final: 0.7144 (m-40) REVERT: B 163 ASP cc_start: 0.8209 (m-30) cc_final: 0.7660 (m-30) REVERT: C 26 SER cc_start: 0.8067 (t) cc_final: 0.7807 (p) REVERT: D 94 MET cc_start: 0.6725 (mtt) cc_final: 0.6085 (mpt) outliers start: 24 outliers final: 10 residues processed: 135 average time/residue: 1.0332 time to fit residues: 151.0588 Evaluate side-chains 139 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9692 Z= 0.173 Angle : 0.458 6.069 13250 Z= 0.248 Chirality : 0.040 0.155 1501 Planarity : 0.003 0.028 1614 Dihedral : 8.779 73.509 1534 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.41 % Allowed : 15.04 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.57 (0.25), residues: 1110 helix: 0.77 (0.23), residues: 512 sheet: 0.22 (0.45), residues: 122 loop : 0.17 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 916 HIS 0.003 0.001 HIS A 613 PHE 0.018 0.001 PHE A 652 TYR 0.011 0.001 TYR A 788 ARG 0.005 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8387 (t) cc_final: 0.8121 (p) REVERT: A 98 LYS cc_start: 0.8345 (tttt) cc_final: 0.8099 (tttm) REVERT: A 855 MET cc_start: 0.7928 (mtm) cc_final: 0.7575 (ttm) REVERT: B 100 ASN cc_start: 0.7440 (p0) cc_final: 0.7172 (m-40) REVERT: B 163 ASP cc_start: 0.8143 (m-30) cc_final: 0.7617 (m-30) REVERT: C 26 SER cc_start: 0.7969 (t) cc_final: 0.7746 (p) REVERT: C 60 LEU cc_start: 0.7787 (mt) cc_final: 0.7514 (mp) REVERT: D 94 MET cc_start: 0.6693 (mtt) cc_final: 0.6018 (mpt) outliers start: 14 outliers final: 10 residues processed: 138 average time/residue: 1.0161 time to fit residues: 152.3617 Evaluate side-chains 138 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 169 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.0470 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9692 Z= 0.243 Angle : 0.501 11.210 13250 Z= 0.267 Chirality : 0.041 0.151 1501 Planarity : 0.003 0.028 1614 Dihedral : 8.764 73.653 1534 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.12 % Allowed : 14.93 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1110 helix: 0.80 (0.23), residues: 507 sheet: 0.20 (0.45), residues: 122 loop : 0.10 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 182 HIS 0.003 0.001 HIS A 613 PHE 0.020 0.001 PHE A 652 TYR 0.012 0.001 TYR A 748 ARG 0.005 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8440 (t) cc_final: 0.8137 (p) REVERT: A 98 LYS cc_start: 0.8377 (tttt) cc_final: 0.8131 (tttm) REVERT: A 855 MET cc_start: 0.7986 (mtm) cc_final: 0.7658 (ttm) REVERT: B 100 ASN cc_start: 0.7492 (p0) cc_final: 0.7200 (m-40) REVERT: B 163 ASP cc_start: 0.8116 (m-30) cc_final: 0.7586 (m-30) REVERT: C 13 LEU cc_start: 0.8265 (tp) cc_final: 0.7986 (tt) REVERT: C 26 SER cc_start: 0.7990 (t) cc_final: 0.7763 (p) REVERT: C 60 LEU cc_start: 0.7781 (mt) cc_final: 0.7531 (mp) outliers start: 21 outliers final: 13 residues processed: 144 average time/residue: 1.0302 time to fit residues: 160.5510 Evaluate side-chains 144 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9692 Z= 0.206 Angle : 0.482 8.486 13250 Z= 0.257 Chirality : 0.040 0.144 1501 Planarity : 0.003 0.028 1614 Dihedral : 8.691 73.574 1534 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.61 % Allowed : 15.64 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.25), residues: 1110 helix: 0.80 (0.23), residues: 509 sheet: 0.17 (0.45), residues: 122 loop : 0.01 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 182 HIS 0.003 0.001 HIS A 613 PHE 0.019 0.001 PHE A 652 TYR 0.011 0.001 TYR A 748 ARG 0.005 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8430 (t) cc_final: 0.8121 (p) REVERT: A 855 MET cc_start: 0.8011 (mtm) cc_final: 0.7676 (ttm) REVERT: B 100 ASN cc_start: 0.7548 (p0) cc_final: 0.7232 (m-40) REVERT: B 163 ASP cc_start: 0.8000 (m-30) cc_final: 0.7514 (m-30) REVERT: C 26 SER cc_start: 0.7987 (t) cc_final: 0.7753 (p) REVERT: C 60 LEU cc_start: 0.7762 (mt) cc_final: 0.7535 (mp) REVERT: C 62 MET cc_start: 0.7330 (ppp) cc_final: 0.7129 (pp-130) REVERT: D 94 MET cc_start: 0.6508 (mtt) cc_final: 0.5973 (mpt) outliers start: 16 outliers final: 11 residues processed: 143 average time/residue: 0.9995 time to fit residues: 154.9431 Evaluate side-chains 139 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9692 Z= 0.223 Angle : 0.499 13.212 13250 Z= 0.263 Chirality : 0.041 0.143 1501 Planarity : 0.003 0.028 1614 Dihedral : 8.694 73.607 1534 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.82 % Allowed : 15.84 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.25), residues: 1110 helix: 0.81 (0.23), residues: 507 sheet: 0.26 (0.45), residues: 124 loop : 0.05 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 182 HIS 0.003 0.001 HIS A 613 PHE 0.019 0.001 PHE A 652 TYR 0.012 0.001 TYR A 748 ARG 0.005 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8441 (t) cc_final: 0.8131 (p) REVERT: A 855 MET cc_start: 0.8014 (mtm) cc_final: 0.7676 (ttm) REVERT: B 100 ASN cc_start: 0.7541 (p0) cc_final: 0.7239 (m-40) REVERT: B 163 ASP cc_start: 0.7979 (m-30) cc_final: 0.7453 (m-30) REVERT: C 26 SER cc_start: 0.7980 (t) cc_final: 0.7746 (p) outliers start: 18 outliers final: 12 residues processed: 137 average time/residue: 1.0147 time to fit residues: 150.9193 Evaluate side-chains 130 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9692 Z= 0.145 Angle : 0.461 7.715 13250 Z= 0.245 Chirality : 0.039 0.148 1501 Planarity : 0.003 0.029 1614 Dihedral : 8.608 73.417 1534 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.72 % Allowed : 16.35 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.42 (0.25), residues: 1110 helix: 0.71 (0.23), residues: 522 sheet: 0.07 (0.47), residues: 112 loop : 0.02 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 182 HIS 0.003 0.000 HIS A 613 PHE 0.017 0.001 PHE A 652 TYR 0.011 0.001 TYR A 788 ARG 0.005 0.000 ARG A 889 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8347 (t) cc_final: 0.8058 (p) REVERT: A 855 MET cc_start: 0.7998 (mtm) cc_final: 0.7678 (ttm) REVERT: B 100 ASN cc_start: 0.7529 (p0) cc_final: 0.7261 (m-40) REVERT: B 163 ASP cc_start: 0.7929 (m-30) cc_final: 0.7408 (m-30) REVERT: D 94 MET cc_start: 0.6447 (mtt) cc_final: 0.5951 (mpt) outliers start: 17 outliers final: 11 residues processed: 128 average time/residue: 1.0757 time to fit residues: 149.3274 Evaluate side-chains 135 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.127830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.082568 restraints weight = 13202.639| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.19 r_work: 0.2871 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9692 Z= 0.262 Angle : 0.528 13.170 13250 Z= 0.277 Chirality : 0.041 0.148 1501 Planarity : 0.003 0.028 1614 Dihedral : 8.710 73.665 1534 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.11 % Allowed : 16.95 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.43 (0.25), residues: 1110 helix: 0.79 (0.23), residues: 513 sheet: -0.05 (0.44), residues: 132 loop : -0.02 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 182 HIS 0.003 0.001 HIS A 99 PHE 0.020 0.001 PHE A 652 TYR 0.021 0.002 TYR B 135 ARG 0.005 0.000 ARG A 889 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3801.97 seconds wall clock time: 67 minutes 38.62 seconds (4058.62 seconds total)