Starting phenix.real_space_refine on Mon Apr 8 16:54:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9v_36116/04_2024/8j9v_36116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9v_36116/04_2024/8j9v_36116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9v_36116/04_2024/8j9v_36116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9v_36116/04_2024/8j9v_36116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9v_36116/04_2024/8j9v_36116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9v_36116/04_2024/8j9v_36116_updated.pdb" } resolution = 2.71 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 8732 2.51 5 N 2396 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 13918 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6307 Classifications: {'peptide': 778} Link IDs: {'PTRANS': 30, 'TRANS': 747} Chain: "B" Number of atoms: 6307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6307 Classifications: {'peptide': 778} Link IDs: {'PTRANS': 30, 'TRANS': 747} Chain: "C" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "E" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 338 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "F" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 338 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.69, per 1000 atoms: 0.55 Number of scatterers: 13918 At special positions: 0 Unit cell: (97.11, 126.99, 117.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 56 15.00 Mg 2 11.99 O 2676 8.00 N 2396 7.00 C 8732 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: 6.05 Conformation dependent library (CDL) restraints added in 2.3 seconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 14 sheets defined 45.9% alpha, 9.8% beta 15 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 6.87 Creating SS restraints... Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 497 through 500 No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 622 through 631 removed outlier: 3.556A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.989A pdb=" N LYS A 646 " --> pdb=" O ASP A 643 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 647 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 652 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 661 No H-bonds generated for 'chain 'A' and resid 658 through 661' Processing helix chain 'A' and resid 673 through 681 Processing helix chain 'A' and resid 687 through 706 removed outlier: 3.842A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.826A pdb=" N LEU A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'A' and resid 867 through 876 Processing helix chain 'A' and resid 883 through 892 Processing helix chain 'A' and resid 945 through 952 Processing helix chain 'A' and resid 954 through 958 removed outlier: 3.575A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 954 through 958' Processing helix chain 'A' and resid 982 through 990 removed outlier: 3.996A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1028 through 1074 Proline residue: A1037 - end of helix removed outlier: 5.186A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1082 through 1092 Processing helix chain 'A' and resid 1099 through 1103 Processing helix chain 'A' and resid 1110 through 1117 Processing helix chain 'A' and resid 1123 through 1127 Processing helix chain 'A' and resid 1130 through 1133 Processing helix chain 'A' and resid 1135 through 1160 removed outlier: 3.734A pdb=" N GLN A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1187 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 477 through 479 No H-bonds generated for 'chain 'B' and resid 477 through 479' Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 497 through 500 No H-bonds generated for 'chain 'B' and resid 497 through 500' Processing helix chain 'B' and resid 503 through 512 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 622 through 631 removed outlier: 3.552A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 652 removed outlier: 3.982A pdb=" N LYS B 646 " --> pdb=" O ASP B 643 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 652 " --> pdb=" O PHE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 661 No H-bonds generated for 'chain 'B' and resid 658 through 661' Processing helix chain 'B' and resid 673 through 681 Processing helix chain 'B' and resid 687 through 706 removed outlier: 3.849A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 756 through 766 Processing helix chain 'B' and resid 798 through 800 No H-bonds generated for 'chain 'B' and resid 798 through 800' Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 821 removed outlier: 3.852A pdb=" N LEU B 821 " --> pdb=" O GLU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 845 No H-bonds generated for 'chain 'B' and resid 843 through 845' Processing helix chain 'B' and resid 867 through 876 Processing helix chain 'B' and resid 883 through 892 Processing helix chain 'B' and resid 945 through 952 Processing helix chain 'B' and resid 954 through 958 removed outlier: 3.623A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 954 through 958' Processing helix chain 'B' and resid 982 through 990 removed outlier: 3.986A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1003 Processing helix chain 'B' and resid 1028 through 1074 Proline residue: B1037 - end of helix removed outlier: 5.187A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1082 through 1092 Processing helix chain 'B' and resid 1099 through 1103 Processing helix chain 'B' and resid 1110 through 1117 Processing helix chain 'B' and resid 1123 through 1127 Processing helix chain 'B' and resid 1130 through 1133 Processing helix chain 'B' and resid 1135 through 1160 removed outlier: 3.740A pdb=" N GLN B1160 " --> pdb=" O GLU B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1167 through 1187 Processing sheet with id= A, first strand: chain 'A' and resid 465 through 469 removed outlier: 6.485A pdb=" N MET A 433 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE A 468 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU A 435 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS A 533 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA A 436 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 535 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 577 through 581 Processing sheet with id= C, first strand: chain 'A' and resid 779 through 782 Processing sheet with id= D, first strand: chain 'A' and resid 849 through 853 Processing sheet with id= E, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.502A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 922 through 926 removed outlier: 3.566A pdb=" N GLU A 936 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP A 924 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 934 " --> pdb=" O ASP A 924 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER A 926 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE A 932 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id= H, first strand: chain 'B' and resid 465 through 469 removed outlier: 6.470A pdb=" N MET B 433 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE B 468 " --> pdb=" O MET B 433 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU B 435 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS B 533 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA B 436 " --> pdb=" O CYS B 533 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL B 535 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 577 through 581 Processing sheet with id= J, first strand: chain 'B' and resid 779 through 782 Processing sheet with id= K, first strand: chain 'B' and resid 849 through 853 Processing sheet with id= L, first strand: chain 'B' and resid 909 through 913 removed outlier: 4.460A pdb=" N TYR B 917 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 922 through 926 removed outlier: 3.567A pdb=" N GLU B 936 " --> pdb=" O THR B 922 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP B 924 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B 934 " --> pdb=" O ASP B 924 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N SER B 926 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE B 932 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 1014 through 1016 481 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 6.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2250 1.32 - 1.44: 4172 1.44 - 1.56: 7746 1.56 - 1.69: 112 1.69 - 1.81: 88 Bond restraints: 14368 Sorted by residual: bond pdb=" CA LEU A 514 " pdb=" C LEU A 514 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.24e-02 6.50e+03 9.43e+00 bond pdb=" N SER A 953 " pdb=" CA SER A 953 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.25e-02 6.40e+03 5.47e+00 bond pdb=" C PRO B1105 " pdb=" O PRO B1105 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.16e-02 7.43e+03 5.46e+00 bond pdb=" C PRO A1105 " pdb=" O PRO A1105 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.16e-02 7.43e+03 5.30e+00 bond pdb=" N SER B 953 " pdb=" CA SER B 953 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.25e-02 6.40e+03 5.22e+00 ... (remaining 14363 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.83: 546 105.83 - 112.86: 7685 112.86 - 119.89: 4837 119.89 - 126.92: 6303 126.92 - 133.95: 313 Bond angle restraints: 19684 Sorted by residual: angle pdb=" N SER A 954 " pdb=" CA SER A 954 " pdb=" C SER A 954 " ideal model delta sigma weight residual 111.07 117.22 -6.15 1.07e+00 8.73e-01 3.31e+01 angle pdb=" N SER B 954 " pdb=" CA SER B 954 " pdb=" C SER B 954 " ideal model delta sigma weight residual 111.07 117.01 -5.94 1.07e+00 8.73e-01 3.08e+01 angle pdb=" N PRO A1105 " pdb=" CA PRO A1105 " pdb=" C PRO A1105 " ideal model delta sigma weight residual 113.57 107.52 6.05 1.31e+00 5.83e-01 2.13e+01 angle pdb=" C LEU A 514 " pdb=" N ASP A 515 " pdb=" CA ASP A 515 " ideal model delta sigma weight residual 122.87 115.94 6.93 1.61e+00 3.86e-01 1.85e+01 angle pdb=" C GLU B1106 " pdb=" CA GLU B1106 " pdb=" CB GLU B1106 " ideal model delta sigma weight residual 117.23 111.57 5.66 1.36e+00 5.41e-01 1.73e+01 ... (remaining 19679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 8290 35.72 - 71.44: 241 71.44 - 107.16: 5 107.16 - 142.88: 2 142.88 - 178.60: 2 Dihedral angle restraints: 8540 sinusoidal: 3978 harmonic: 4562 Sorted by residual: dihedral pdb=" C4' DA F 9 " pdb=" C3' DA F 9 " pdb=" O3' DA F 9 " pdb=" P DC F 10 " ideal model delta sinusoidal sigma weight residual -140.00 38.60 -178.60 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA D 9 " pdb=" C3' DA D 9 " pdb=" O3' DA D 9 " pdb=" P DC D 10 " ideal model delta sinusoidal sigma weight residual 220.00 41.50 178.50 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA SER A 853 " pdb=" C SER A 853 " pdb=" N GLU A 854 " pdb=" CA GLU A 854 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 8537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1631 0.044 - 0.089: 421 0.089 - 0.133: 98 0.133 - 0.177: 2 0.177 - 0.222: 2 Chirality restraints: 2154 Sorted by residual: chirality pdb=" C9 EVP F 101 " pdb=" C10 EVP F 101 " pdb=" C6 EVP F 101 " pdb=" C8 EVP F 101 " both_signs ideal model delta sigma weight residual False 2.49 2.71 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C9 EVP D 101 " pdb=" C10 EVP D 101 " pdb=" C6 EVP D 101 " pdb=" C8 EVP D 101 " both_signs ideal model delta sigma weight residual False 2.49 2.71 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' DA D 9 " pdb=" C4' DA D 9 " pdb=" O3' DA D 9 " pdb=" C2' DA D 9 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 2151 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 512 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C LEU A 512 " 0.063 2.00e-02 2.50e+03 pdb=" O LEU A 512 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY A 513 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1104 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C SER A1104 " 0.038 2.00e-02 2.50e+03 pdb=" O SER A1104 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO A1105 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 937 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 938 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.026 5.00e-02 4.00e+02 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 170 2.62 - 3.19: 12440 3.19 - 3.76: 22937 3.76 - 4.33: 32010 4.33 - 4.90: 50690 Nonbonded interactions: 118247 Sorted by model distance: nonbonded pdb=" OD2 ASP B 541 " pdb="MG MG B1201 " model vdw 2.053 2.170 nonbonded pdb=" OD2 ASP A 541 " pdb="MG MG A1201 " model vdw 2.053 2.170 nonbonded pdb=" OH TYR B 751 " pdb=" OP2 DG E 12 " model vdw 2.230 2.440 nonbonded pdb=" O PRO A 942 " pdb=" OG1 THR A 943 " model vdw 2.236 2.440 nonbonded pdb=" O PRO B 942 " pdb=" OG1 THR B 943 " model vdw 2.244 2.440 ... (remaining 118242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 4.720 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: 16.670 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 44.060 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.003 0.041 14368 Z= 0.199 Angle : 0.590 8.758 19684 Z= 0.332 Chirality : 0.041 0.222 2154 Planarity : 0.004 0.061 2290 Dihedral : 15.160 178.599 5616 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1552 helix: 1.25 (0.20), residues: 716 sheet: -0.02 (0.36), residues: 184 loop : -0.39 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 560 HIS 0.003 0.001 HIS B1051 PHE 0.011 0.001 PHE B1107 TYR 0.011 0.001 TYR B 698 ARG 0.009 0.000 ARG A1185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: A 1050 GLU cc_start: 0.9042 (tp30) cc_final: 0.8744 (tp30) REVERT: B 1050 GLU cc_start: 0.9056 (tp30) cc_final: 0.8745 (tp30) outliers start: 0 outliers final: 1 residues processed: 57 average time/residue: 2.0243 time to fit residues: 124.6999 Evaluate side-chains 42 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1058 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 0.0470 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 930 ASN B 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14368 Z= 0.219 Angle : 0.517 7.533 19684 Z= 0.276 Chirality : 0.040 0.186 2154 Planarity : 0.004 0.046 2290 Dihedral : 17.122 176.864 2504 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.15 % Allowed : 6.44 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1552 helix: 1.33 (0.20), residues: 728 sheet: -0.40 (0.34), residues: 208 loop : -0.03 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 560 HIS 0.004 0.001 HIS B1099 PHE 0.010 0.001 PHE B1094 TYR 0.013 0.001 TYR A1124 ARG 0.008 0.000 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 929 ARG cc_start: 0.8730 (tpm170) cc_final: 0.8490 (tpm170) REVERT: A 1050 GLU cc_start: 0.9061 (tp30) cc_final: 0.8736 (tp30) REVERT: B 929 ARG cc_start: 0.8723 (tpm170) cc_final: 0.8471 (tpm170) REVERT: B 1050 GLU cc_start: 0.9062 (tp30) cc_final: 0.8758 (tp30) outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 1.6439 time to fit residues: 83.1831 Evaluate side-chains 41 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 690 HIS B1114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14368 Z= 0.298 Angle : 0.540 7.698 19684 Z= 0.289 Chirality : 0.041 0.191 2154 Planarity : 0.004 0.050 2290 Dihedral : 17.168 175.630 2502 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.88 % Allowed : 7.69 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1552 helix: 1.34 (0.20), residues: 724 sheet: -0.51 (0.34), residues: 206 loop : -0.03 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1170 HIS 0.004 0.001 HIS A1099 PHE 0.013 0.001 PHE A1094 TYR 0.014 0.001 TYR A 698 ARG 0.008 0.001 ARG B 863 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 929 ARG cc_start: 0.8751 (tpm170) cc_final: 0.8479 (tpm170) REVERT: A 1050 GLU cc_start: 0.9105 (tp30) cc_final: 0.8830 (tp30) REVERT: B 514 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8572 (pp) REVERT: B 929 ARG cc_start: 0.8755 (tpm170) cc_final: 0.8495 (tpm170) REVERT: B 1050 GLU cc_start: 0.9141 (tp30) cc_final: 0.8864 (tp30) outliers start: 12 outliers final: 1 residues processed: 48 average time/residue: 1.6130 time to fit residues: 85.5906 Evaluate side-chains 43 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14368 Z= 0.178 Angle : 0.485 7.375 19684 Z= 0.260 Chirality : 0.039 0.173 2154 Planarity : 0.003 0.048 2290 Dihedral : 16.846 176.196 2502 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.66 % Allowed : 9.59 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1552 helix: 1.42 (0.20), residues: 724 sheet: -0.47 (0.34), residues: 206 loop : 0.04 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 560 HIS 0.002 0.001 HIS B 566 PHE 0.008 0.001 PHE A 990 TYR 0.012 0.001 TYR A 698 ARG 0.005 0.000 ARG B 863 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: A 929 ARG cc_start: 0.8802 (tpm170) cc_final: 0.8538 (tpm170) REVERT: A 1050 GLU cc_start: 0.9079 (tp30) cc_final: 0.8758 (tp30) REVERT: B 929 ARG cc_start: 0.8786 (tpm170) cc_final: 0.8540 (tpm170) REVERT: B 1050 GLU cc_start: 0.9109 (tp30) cc_final: 0.8806 (tp30) REVERT: B 1173 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8625 (mt-10) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 1.5635 time to fit residues: 84.3537 Evaluate side-chains 46 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14368 Z= 0.315 Angle : 0.541 8.606 19684 Z= 0.288 Chirality : 0.041 0.193 2154 Planarity : 0.004 0.047 2290 Dihedral : 16.889 173.712 2502 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.24 % Allowed : 9.81 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1552 helix: 1.35 (0.20), residues: 724 sheet: -0.61 (0.33), residues: 206 loop : -0.04 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1170 HIS 0.003 0.001 HIS A1099 PHE 0.011 0.001 PHE A 590 TYR 0.014 0.001 TYR A 698 ARG 0.006 0.000 ARG B 863 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 1.557 Fit side-chains revert: symmetry clash REVERT: A 929 ARG cc_start: 0.8848 (tpm170) cc_final: 0.8622 (tpm170) REVERT: A 1050 GLU cc_start: 0.9099 (tp30) cc_final: 0.8828 (tp30) REVERT: B 514 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8712 (pp) REVERT: B 929 ARG cc_start: 0.8798 (tpm170) cc_final: 0.8536 (tpm170) REVERT: B 1050 GLU cc_start: 0.9128 (tp30) cc_final: 0.8868 (tp30) outliers start: 17 outliers final: 7 residues processed: 56 average time/residue: 1.4754 time to fit residues: 91.3594 Evaluate side-chains 48 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.0570 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14368 Z= 0.151 Angle : 0.489 9.525 19684 Z= 0.259 Chirality : 0.038 0.166 2154 Planarity : 0.003 0.048 2290 Dihedral : 16.699 175.804 2502 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.24 % Allowed : 10.25 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1552 helix: 1.45 (0.20), residues: 724 sheet: -0.51 (0.34), residues: 206 loop : 0.03 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1189 HIS 0.002 0.000 HIS B1051 PHE 0.008 0.001 PHE A 990 TYR 0.012 0.001 TYR A 698 ARG 0.003 0.000 ARG B 799 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 929 ARG cc_start: 0.8874 (tpm170) cc_final: 0.8609 (tpm170) REVERT: A 1050 GLU cc_start: 0.9068 (tp30) cc_final: 0.8778 (tp30) REVERT: A 1173 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8582 (mt-10) REVERT: B 514 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8692 (pp) REVERT: B 929 ARG cc_start: 0.8853 (tpm170) cc_final: 0.8595 (tpm170) REVERT: B 1050 GLU cc_start: 0.9109 (tp30) cc_final: 0.8829 (tp30) REVERT: B 1173 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8521 (mt-10) outliers start: 17 outliers final: 7 residues processed: 59 average time/residue: 1.4719 time to fit residues: 95.9614 Evaluate side-chains 51 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14368 Z= 0.322 Angle : 0.548 9.028 19684 Z= 0.288 Chirality : 0.041 0.188 2154 Planarity : 0.004 0.048 2290 Dihedral : 16.847 173.300 2502 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.17 % Allowed : 10.83 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1552 helix: 1.36 (0.20), residues: 724 sheet: -0.66 (0.34), residues: 208 loop : -0.01 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1170 HIS 0.003 0.001 HIS A1099 PHE 0.010 0.001 PHE A 590 TYR 0.014 0.001 TYR A 698 ARG 0.004 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 704 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: A 929 ARG cc_start: 0.8885 (tpm170) cc_final: 0.8621 (tpm170) REVERT: A 1050 GLU cc_start: 0.9088 (tp30) cc_final: 0.8839 (tp30) REVERT: A 1060 MET cc_start: 0.8554 (ttt) cc_final: 0.8336 (ttm) REVERT: B 514 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8699 (pp) REVERT: B 929 ARG cc_start: 0.8864 (tpm170) cc_final: 0.8591 (tpm170) REVERT: B 934 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.9248 (pp) REVERT: B 1050 GLU cc_start: 0.9113 (tp30) cc_final: 0.8869 (tp30) outliers start: 16 outliers final: 9 residues processed: 55 average time/residue: 1.4338 time to fit residues: 88.1295 Evaluate side-chains 53 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1097 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.8233 > 50: distance: 57 - 61: 5.050 distance: 61 - 62: 31.417 distance: 62 - 63: 31.208 distance: 63 - 64: 18.580 distance: 63 - 65: 34.037 distance: 65 - 66: 17.756 distance: 66 - 67: 24.997 distance: 66 - 69: 41.048 distance: 67 - 68: 35.635 distance: 67 - 71: 27.485 distance: 69 - 70: 21.084 distance: 71 - 72: 9.174 distance: 72 - 73: 10.309 distance: 73 - 74: 33.617 distance: 73 - 75: 19.303 distance: 75 - 76: 11.807 distance: 76 - 77: 17.248 distance: 76 - 79: 13.131 distance: 77 - 78: 23.100 distance: 77 - 84: 22.073 distance: 79 - 80: 4.498 distance: 80 - 81: 18.889 distance: 81 - 82: 26.510 distance: 82 - 83: 53.953 distance: 84 - 85: 36.545 distance: 85 - 86: 44.951 distance: 85 - 88: 24.760 distance: 86 - 87: 15.543 distance: 86 - 92: 45.134 distance: 87 - 112: 50.030 distance: 88 - 89: 42.870 distance: 88 - 90: 15.548 distance: 89 - 91: 43.584 distance: 92 - 93: 35.659 distance: 93 - 94: 34.543 distance: 93 - 96: 20.308 distance: 94 - 95: 43.016 distance: 94 - 100: 13.191 distance: 95 - 120: 30.987 distance: 96 - 97: 32.318 distance: 97 - 98: 6.891 distance: 97 - 99: 32.702 distance: 100 - 101: 31.772 distance: 101 - 102: 31.938 distance: 102 - 103: 28.761 distance: 102 - 104: 44.728 distance: 103 - 128: 12.401 distance: 104 - 105: 21.486 distance: 105 - 106: 37.418 distance: 105 - 108: 36.860 distance: 106 - 107: 41.303 distance: 106 - 112: 45.130 distance: 107 - 133: 28.407 distance: 108 - 109: 38.457 distance: 109 - 110: 23.244 distance: 109 - 111: 42.115 distance: 112 - 113: 35.741 distance: 113 - 114: 13.495 distance: 113 - 116: 31.208 distance: 114 - 115: 52.072 distance: 114 - 120: 40.794 distance: 115 - 140: 30.790 distance: 116 - 117: 68.823 distance: 117 - 118: 56.997 distance: 117 - 119: 56.449 distance: 120 - 121: 15.833 distance: 121 - 122: 35.815 distance: 121 - 124: 10.969 distance: 122 - 123: 28.686 distance: 122 - 128: 15.052 distance: 123 - 149: 30.655 distance: 124 - 125: 36.849 distance: 125 - 126: 16.366 distance: 125 - 127: 20.261