Starting phenix.real_space_refine on Mon Apr 8 02:40:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo7_26641/04_2024/7uo7_26641_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo7_26641/04_2024/7uo7_26641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo7_26641/04_2024/7uo7_26641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo7_26641/04_2024/7uo7_26641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo7_26641/04_2024/7uo7_26641_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo7_26641/04_2024/7uo7_26641_neut_updated.pdb" } resolution = 3.09 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= -0.001 sd= 0.032 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 Zn 2 6.06 5 P 69 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 7517 2.51 5 N 2071 2.21 5 O 2520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 665": "OE1" <-> "OE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12262 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Chain: "B" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1390 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "P" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 676 Classifications: {'RNA': 32} Modifications used: {'rna3p_pur': 14, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 722 Classifications: {'RNA': 34} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 32} Chain: "D" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1419 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 53.440 29.475 112.645 1.00 48.49 S ATOM 2487 SG CYS A 306 51.427 26.240 112.674 1.00 49.42 S ATOM 2519 SG CYS A 310 51.496 29.227 114.986 1.00 46.57 S ATOM 3927 SG CYS A 487 55.042 32.825 92.691 1.00 55.11 S ATOM 5180 SG CYS A 645 54.189 29.318 92.380 1.00 57.31 S ATOM 5186 SG CYS A 646 56.390 31.133 95.014 1.00 53.98 S Time building chain proxies: 7.09, per 1000 atoms: 0.58 Number of scatterers: 12262 At special positions: 0 Unit cell: (91.46, 130.196, 165.704, 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) Zn 2 29.99 S 82 16.00 P 69 15.00 Mg 1 11.99 O 2520 8.00 N 2071 7.00 C 7517 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: 5.50 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 301 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 645 " Number of angles added : 6 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 13 sheets defined 47.2% alpha, 7.5% beta 30 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 198 removed outlier: 3.635A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS A 188 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR A 189 " --> pdb=" O LEU A 186 " (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 242 through 247 removed outlier: 3.701A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' 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 307 No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 310 through 317 removed outlier: 4.105A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.885A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.084A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (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 517 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 580 removed outlier: 4.006A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.701A 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 637 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.617A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.971A pdb=" N GLU A 744 " --> pdb=" O ASP A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 857 through 871 Proline residue: A 868 - end of helix removed outlier: 4.491A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.880A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 914 removed outlier: 3.864A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 914' Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.993A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 96 removed outlier: 4.015A pdb=" N LEU B 38 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 47 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU B 48 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.968A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 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 2 through 20 removed outlier: 3.865A pdb=" N VAL C 6 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS C 7 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.661A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 81 Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing sheet with id= A, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 55 through 57 Processing sheet with id= C, first strand: chain 'A' and resid 100 through 105 removed outlier: 4.038A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 111 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 201 through 203 Processing sheet with id= E, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= F, first strand: chain 'A' and resid 345 through 347 Processing sheet with id= G, first strand: chain 'A' and resid 541 through 544 removed outlier: 3.669A pdb=" N GLN A 541 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 800 through 802 removed outlier: 3.619A pdb=" N TRP A 800 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.592A pdb=" N GLN A 822 " --> pdb=" O ASP A 825 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.850A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 130 through 132 Processing sheet with id= L, first strand: chain 'B' and resid 146 through 148 Processing sheet with id= M, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.905A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 5.95 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: 3624 1.34 - 1.45: 2362 1.45 - 1.57: 6407 1.57 - 1.69: 132 1.69 - 1.81: 128 Bond restraints: 12653 Sorted by residual: bond pdb=" C TRP A 617 " pdb=" N ASP A 618 " ideal model delta sigma weight residual 1.331 1.571 -0.239 1.29e-02 6.01e+03 3.43e+02 bond pdb=" C ASP A 618 " pdb=" N TYR A 619 " ideal model delta sigma weight residual 1.328 1.582 -0.254 1.44e-02 4.82e+03 3.12e+02 bond pdb=" C4 ATP A1001 " pdb=" N9 ATP A1001 " ideal model delta sigma weight residual 1.374 1.232 0.142 1.00e-02 1.00e+04 2.03e+02 bond pdb=" C3' ATP A1001 " pdb=" C4' ATP A1001 " ideal model delta sigma weight residual 1.526 1.412 0.114 1.10e-02 8.26e+03 1.07e+02 bond pdb=" C5 ATP A1001 " pdb=" N7 ATP A1001 " ideal model delta sigma weight residual 1.387 1.301 0.086 1.00e-02 1.00e+04 7.35e+01 ... (remaining 12648 not shown) Histogram of bond angle deviations from ideal: 92.37 - 101.76: 110 101.76 - 111.15: 5545 111.15 - 120.55: 7301 120.55 - 129.94: 4436 129.94 - 139.33: 89 Bond angle restraints: 17481 Sorted by residual: angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 124.89 14.98 1.00e+00 1.00e+00 2.24e+02 angle pdb=" C3' ATP A1001 " pdb=" C4' ATP A1001 " pdb=" C5' ATP A1001 " ideal model delta sigma weight residual 115.19 96.10 19.09 1.76e+00 3.23e-01 1.18e+02 angle pdb=" O TRP A 617 " pdb=" C TRP A 617 " pdb=" N ASP A 618 " ideal model delta sigma weight residual 123.46 133.34 -9.88 9.90e-01 1.02e+00 9.96e+01 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 128.28 8.55 1.00e+00 1.00e+00 7.31e+01 angle pdb=" CA TRP A 617 " pdb=" C TRP A 617 " pdb=" N ASP A 618 " ideal model delta sigma weight residual 115.38 104.51 10.87 1.40e+00 5.10e-01 6.03e+01 ... (remaining 17476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.21: 7380 31.21 - 62.41: 236 62.41 - 93.62: 63 93.62 - 124.83: 1 124.83 - 156.04: 2 Dihedral angle restraints: 7682 sinusoidal: 3607 harmonic: 4075 Sorted by residual: dihedral pdb=" CA HIS A 613 " pdb=" C HIS A 613 " pdb=" N LEU A 614 " pdb=" CA LEU A 614 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA PRO A 612 " pdb=" C PRO A 612 " pdb=" N HIS A 613 " pdb=" CA HIS A 613 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" C4' C T 19 " pdb=" C3' C T 19 " pdb=" O3' C T 19 " pdb=" P U T 20 " ideal model delta sinusoidal sigma weight residual -110.00 46.04 -156.04 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1921 0.082 - 0.164: 104 0.164 - 0.247: 1 0.247 - 0.329: 1 0.329 - 0.411: 1 Chirality restraints: 2028 Sorted by residual: chirality pdb=" C3' ATP A1001 " pdb=" C2' ATP A1001 " pdb=" C4' ATP A1001 " pdb=" O3' ATP A1001 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C2' ATP A1001 " pdb=" C1' ATP A1001 " pdb=" C3' ATP A1001 " pdb=" O2' ATP A1001 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C3' C T 19 " pdb=" C4' C T 19 " pdb=" O3' C T 19 " pdb=" C2' C T 19 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 2025 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 618 " -0.044 2.00e-02 2.50e+03 8.51e-02 7.24e+01 pdb=" C ASP A 618 " 0.147 2.00e-02 2.50e+03 pdb=" O ASP A 618 " -0.060 2.00e-02 2.50e+03 pdb=" N TYR A 619 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 178 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 42 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C LEU D 42 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU D 42 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN D 43 " 0.009 2.00e-02 2.50e+03 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 158 2.59 - 3.17: 11290 3.17 - 3.74: 20038 3.74 - 4.32: 28629 4.32 - 4.90: 45579 Nonbonded interactions: 105694 Sorted by model distance: nonbonded pdb=" OD2 ASP A 833 " pdb=" OG SER A 835 " model vdw 2.012 2.440 nonbonded pdb=" OG SER A 433 " pdb=" OE2 GLU A 436 " model vdw 2.027 2.440 nonbonded pdb=" OD2 ASP A 452 " pdb=" OG1 THR A 556 " model vdw 2.028 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG SER B 164 " model vdw 2.058 2.440 nonbonded pdb=" OG1 THR A 409 " pdb=" OE2 GLU C 23 " model vdw 2.077 2.440 ... (remaining 105689 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 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 50 or (resid 51 and (name N or name CA or \ name C or name O or name CB )) or resid 52 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 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: 12.410 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 42.850 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 0.254 12653 Z= 0.360 Angle : 0.640 19.089 17481 Z= 0.394 Chirality : 0.038 0.411 2028 Planarity : 0.004 0.085 1989 Dihedral : 15.461 156.036 5044 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.76 % Allowed : 6.94 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.61 (0.22), residues: 1363 helix: -0.32 (0.21), residues: 676 sheet: -2.06 (0.45), residues: 130 loop : -1.65 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.013 0.001 PHE D 49 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 LYS cc_start: 0.8468 (tptt) cc_final: 0.8233 (mmtt) outliers start: 9 outliers final: 4 residues processed: 113 average time/residue: 0.2641 time to fit residues: 43.4333 Evaluate side-chains 80 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS A 892 HIS A 909 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12653 Z= 0.256 Angle : 0.555 8.848 17481 Z= 0.290 Chirality : 0.040 0.208 2028 Planarity : 0.004 0.046 1989 Dihedral : 15.830 157.126 2544 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.52 % Allowed : 9.40 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.18 (0.22), residues: 1363 helix: -0.01 (0.20), residues: 672 sheet: -2.02 (0.48), residues: 110 loop : -1.36 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 182 HIS 0.007 0.001 HIS A 613 PHE 0.019 0.002 PHE D 15 TYR 0.012 0.001 TYR A 921 ARG 0.002 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7394 (ttm) cc_final: 0.7062 (ttm) outliers start: 18 outliers final: 8 residues processed: 101 average time/residue: 0.2433 time to fit residues: 36.2386 Evaluate side-chains 87 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12653 Z= 0.201 Angle : 0.512 8.553 17481 Z= 0.270 Chirality : 0.038 0.209 2028 Planarity : 0.004 0.043 1989 Dihedral : 15.794 158.527 2541 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.86 % Allowed : 10.67 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.97 (0.22), residues: 1363 helix: 0.12 (0.20), residues: 679 sheet: -1.96 (0.45), residues: 118 loop : -1.17 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 182 HIS 0.006 0.001 HIS A 613 PHE 0.013 0.001 PHE D 15 TYR 0.011 0.001 TYR A 921 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7409 (ttm) cc_final: 0.7017 (ttm) REVERT: A 909 ASN cc_start: 0.6748 (OUTLIER) cc_final: 0.6396 (p0) REVERT: D 135 TYR cc_start: 0.7103 (t80) cc_final: 0.6519 (t80) REVERT: D 166 ILE cc_start: 0.8855 (mm) cc_final: 0.8412 (mt) outliers start: 22 outliers final: 8 residues processed: 102 average time/residue: 0.2652 time to fit residues: 41.0611 Evaluate side-chains 87 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12653 Z= 0.404 Angle : 0.613 8.819 17481 Z= 0.322 Chirality : 0.042 0.212 2028 Planarity : 0.005 0.042 1989 Dihedral : 15.911 155.071 2541 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.05 % Allowed : 11.52 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.27 (0.22), residues: 1363 helix: -0.11 (0.20), residues: 668 sheet: -2.25 (0.42), residues: 143 loop : -1.22 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 154 HIS 0.007 0.001 HIS C 36 PHE 0.019 0.002 PHE A 504 TYR 0.015 0.002 TYR A 748 ARG 0.005 0.000 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 79 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7597 (ttm) cc_final: 0.7089 (ttm) REVERT: A 909 ASN cc_start: 0.6732 (OUTLIER) cc_final: 0.6425 (p0) REVERT: B 129 MET cc_start: 0.7750 (ttm) cc_final: 0.7543 (mtm) REVERT: D 48 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8389 (tp30) REVERT: D 87 MET cc_start: 0.8285 (tpp) cc_final: 0.8002 (tpp) outliers start: 36 outliers final: 19 residues processed: 114 average time/residue: 0.2310 time to fit residues: 40.1300 Evaluate side-chains 93 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 30.0000 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 0.4980 chunk 94 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 468 GLN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12653 Z= 0.180 Angle : 0.516 11.733 17481 Z= 0.269 Chirality : 0.038 0.207 2028 Planarity : 0.004 0.040 1989 Dihedral : 15.864 156.294 2541 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.54 % Allowed : 13.04 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.23), residues: 1363 helix: 0.11 (0.20), residues: 676 sheet: -1.92 (0.48), residues: 110 loop : -1.08 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.014 0.001 PHE D 15 TYR 0.012 0.001 TYR A 921 ARG 0.002 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7661 (ttm) cc_final: 0.7267 (ttm) REVERT: A 909 ASN cc_start: 0.6426 (OUTLIER) cc_final: 0.6185 (p0) REVERT: D 87 MET cc_start: 0.8148 (tpp) cc_final: 0.7833 (tpp) outliers start: 30 outliers final: 16 residues processed: 111 average time/residue: 0.2222 time to fit residues: 38.7968 Evaluate side-chains 93 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 459 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12653 Z= 0.248 Angle : 0.542 9.235 17481 Z= 0.282 Chirality : 0.039 0.203 2028 Planarity : 0.004 0.033 1989 Dihedral : 15.786 154.594 2541 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.05 % Allowed : 13.89 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.97 (0.22), residues: 1363 helix: 0.05 (0.20), residues: 683 sheet: -1.95 (0.45), residues: 127 loop : -1.07 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS A 613 PHE 0.013 0.001 PHE A 471 TYR 0.010 0.001 TYR D 135 ARG 0.002 0.000 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 77 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7613 (ttm) cc_final: 0.7160 (ttm) REVERT: A 909 ASN cc_start: 0.6501 (OUTLIER) cc_final: 0.6267 (p0) REVERT: D 87 MET cc_start: 0.8205 (tpp) cc_final: 0.7931 (tpp) outliers start: 36 outliers final: 19 residues processed: 109 average time/residue: 0.2156 time to fit residues: 36.9242 Evaluate side-chains 96 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12653 Z= 0.273 Angle : 0.543 9.016 17481 Z= 0.284 Chirality : 0.040 0.238 2028 Planarity : 0.004 0.031 1989 Dihedral : 15.823 153.633 2541 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 3.05 % Allowed : 14.31 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.87 (0.22), residues: 1363 helix: 0.12 (0.20), residues: 675 sheet: -1.84 (0.45), residues: 127 loop : -0.99 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS A 613 PHE 0.015 0.001 PHE A 471 TYR 0.010 0.001 TYR A 748 ARG 0.003 0.000 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 75 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7697 (ttm) cc_final: 0.7251 (ttm) REVERT: A 909 ASN cc_start: 0.6497 (OUTLIER) cc_final: 0.6266 (p0) REVERT: D 87 MET cc_start: 0.8208 (tpp) cc_final: 0.7923 (tpp) outliers start: 36 outliers final: 26 residues processed: 107 average time/residue: 0.2074 time to fit residues: 34.9597 Evaluate side-chains 102 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12653 Z= 0.286 Angle : 0.560 9.100 17481 Z= 0.290 Chirality : 0.040 0.215 2028 Planarity : 0.004 0.029 1989 Dihedral : 15.851 152.890 2541 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 2.96 % Allowed : 14.31 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.80 (0.23), residues: 1363 helix: 0.14 (0.20), residues: 673 sheet: -1.70 (0.51), residues: 110 loop : -0.99 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS A 613 PHE 0.013 0.001 PHE D 92 TYR 0.011 0.001 TYR A 748 ARG 0.003 0.000 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 77 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7653 (ttm) cc_final: 0.7138 (ttm) REVERT: A 909 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.6194 (p0) REVERT: D 48 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8630 (tp30) REVERT: D 87 MET cc_start: 0.8226 (tpp) cc_final: 0.7983 (tpp) outliers start: 35 outliers final: 29 residues processed: 106 average time/residue: 0.2234 time to fit residues: 37.0112 Evaluate side-chains 106 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 55 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12653 Z= 0.198 Angle : 0.536 10.174 17481 Z= 0.276 Chirality : 0.039 0.202 2028 Planarity : 0.004 0.028 1989 Dihedral : 15.833 153.764 2541 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 2.79 % Allowed : 14.31 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.67 (0.23), residues: 1363 helix: 0.28 (0.20), residues: 674 sheet: -1.65 (0.46), residues: 127 loop : -0.91 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.013 0.001 PHE D 15 TYR 0.010 0.001 TYR A 515 ARG 0.001 0.000 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 78 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 909 ASN cc_start: 0.6399 (OUTLIER) cc_final: 0.6168 (p0) REVERT: D 48 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8643 (tp30) REVERT: D 87 MET cc_start: 0.8152 (tpp) cc_final: 0.7886 (tpp) REVERT: D 157 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7436 (mm-40) outliers start: 33 outliers final: 26 residues processed: 105 average time/residue: 0.2106 time to fit residues: 34.8139 Evaluate side-chains 104 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 111 optimal weight: 0.4980 chunk 11 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12653 Z= 0.205 Angle : 0.533 9.250 17481 Z= 0.275 Chirality : 0.038 0.201 2028 Planarity : 0.004 0.028 1989 Dihedral : 15.804 153.057 2541 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.45 % Rotamer: Outliers : 2.54 % Allowed : 15.07 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.61 (0.23), residues: 1363 helix: 0.32 (0.20), residues: 674 sheet: -1.60 (0.46), residues: 127 loop : -0.87 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.013 0.001 PHE A 471 TYR 0.010 0.001 TYR A 515 ARG 0.001 0.000 ARG A 858 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 909 ASN cc_start: 0.6305 (OUTLIER) cc_final: 0.6084 (p0) REVERT: D 48 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8661 (tp30) outliers start: 30 outliers final: 27 residues processed: 102 average time/residue: 0.2298 time to fit residues: 36.2292 Evaluate side-chains 102 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 74 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.0020 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 80 optimal weight: 0.0770 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.068581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.049577 restraints weight = 49101.884| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.46 r_work: 0.3148 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12653 Z= 0.151 Angle : 0.513 9.009 17481 Z= 0.264 Chirality : 0.037 0.200 2028 Planarity : 0.003 0.029 1989 Dihedral : 15.736 153.803 2541 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 2.46 % Allowed : 15.24 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.38 (0.23), residues: 1363 helix: 0.45 (0.21), residues: 673 sheet: -1.44 (0.49), residues: 110 loop : -0.73 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 613 PHE 0.013 0.001 PHE D 15 TYR 0.011 0.001 TYR A 515 ARG 0.001 0.000 ARG A 654 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2525.19 seconds wall clock time: 46 minutes 59.48 seconds (2819.48 seconds total)