Starting phenix.real_space_refine on Tue Jun 10 14:25:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cze_27096/06_2025/8cze_27096.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cze_27096/06_2025/8cze_27096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cze_27096/06_2025/8cze_27096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cze_27096/06_2025/8cze_27096.map" model { file = "/net/cci-nas-00/data/ceres_data/8cze_27096/06_2025/8cze_27096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cze_27096/06_2025/8cze_27096.cif" } resolution = 2.58 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= 0.034 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 12 5.16 5 C 6646 2.51 5 N 2258 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12029 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3009 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2977 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 7.60, per 1000 atoms: 0.63 Number of scatterers: 12029 At special positions: 0 Unit cell: (79.2, 118.8, 126.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 292 15.00 O 2821 8.00 N 2258 7.00 C 6646 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 - 3.00 Amino acid : True - 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: 2.95 Conformation dependent library (CDL) restraints added in 873.2 milliseconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 72.1% alpha, 2.6% beta 133 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.520A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.845A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 4.352A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.720A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.523A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.378A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.668A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.541A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.568A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.863A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.525A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.859A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.520A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.846A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.352A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.719A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.523A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.378A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.668A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.541A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.568A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.862A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.525A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.858A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.989A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.511A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.717A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.385A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.008A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.557A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.417A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 374 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 3.28 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: 2427 1.34 - 1.45: 4063 1.45 - 1.57: 5743 1.57 - 1.69: 582 1.69 - 1.81: 22 Bond restraints: 12837 Sorted by residual: bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" C GLU C 61 " pdb=" O GLU C 61 " ideal model delta sigma weight residual 1.236 1.249 -0.013 1.15e-02 7.56e+03 1.23e+00 bond pdb=" C GLU G 61 " pdb=" O GLU G 61 " ideal model delta sigma weight residual 1.236 1.249 -0.012 1.15e-02 7.56e+03 1.15e+00 bond pdb=" C3' DC I 30 " pdb=" C2' DC I 30 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.08e+00 bond pdb=" C3' DC J 21 " pdb=" C2' DC J 21 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 12832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 17331 1.03 - 2.05: 1005 2.05 - 3.08: 243 3.08 - 4.11: 8 4.11 - 5.13: 8 Bond angle restraints: 18595 Sorted by residual: angle pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sigma weight residual 120.20 123.32 -3.12 1.50e+00 4.44e-01 4.32e+00 angle pdb=" N LYS B 31 " pdb=" CA LYS B 31 " pdb=" C LYS B 31 " ideal model delta sigma weight residual 109.81 114.04 -4.23 2.21e+00 2.05e-01 3.66e+00 angle pdb=" N LYS F 31 " pdb=" CA LYS F 31 " pdb=" C LYS F 31 " ideal model delta sigma weight residual 109.81 114.01 -4.20 2.21e+00 2.05e-01 3.61e+00 angle pdb=" O4' DC I -25 " pdb=" C1' DC I -25 " pdb=" C2' DC I -25 " ideal model delta sigma weight residual 106.40 103.60 2.80 1.50e+00 4.44e-01 3.49e+00 angle pdb=" C3' DC I -40 " pdb=" C2' DC I -40 " pdb=" C1' DC I -40 " ideal model delta sigma weight residual 101.60 104.36 -2.76 1.50e+00 4.44e-01 3.38e+00 ... (remaining 18590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.85: 5600 33.85 - 67.70: 1366 67.70 - 101.55: 3 101.55 - 135.40: 0 135.40 - 169.24: 1 Dihedral angle restraints: 6970 sinusoidal: 4755 harmonic: 2215 Sorted by residual: dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 50.76 169.24 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 165.25 14.75 0 5.00e+00 4.00e-02 8.70e+00 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual 180.00 165.28 14.72 0 5.00e+00 4.00e-02 8.67e+00 ... (remaining 6967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1409 0.026 - 0.052: 482 0.052 - 0.079: 164 0.079 - 0.105: 38 0.105 - 0.131: 30 Chirality restraints: 2123 Sorted by residual: chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 2120 not shown) Planarity restraints: 1341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -49 " 0.025 2.00e-02 2.50e+03 1.06e-02 3.39e+00 pdb=" N9 DG J -49 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG J -49 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG J -49 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG J -49 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -49 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG J -49 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG J -49 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG J -49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG J -49 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.022 2.00e-02 2.50e+03 9.85e-03 2.67e+00 pdb=" N9 DA I 47 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.022 2.00e-02 2.50e+03 9.05e-03 2.45e+00 pdb=" N9 DG I -35 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.001 2.00e-02 2.50e+03 ... (remaining 1338 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2335 2.81 - 3.33: 9353 3.33 - 3.85: 20452 3.85 - 4.38: 25395 4.38 - 4.90: 36571 Nonbonded interactions: 94106 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.285 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.286 3.120 nonbonded pdb=" OD1 ASP C 90 " pdb=" N GLU C 91 " model vdw 2.350 3.120 nonbonded pdb=" OD1 ASP G 90 " pdb=" N GLU G 91 " model vdw 2.351 3.120 nonbonded pdb=" O THR G 10 " pdb=" OG1 THR G 10 " model vdw 2.381 3.040 ... (remaining 94101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.680 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.190 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12837 Z= 0.174 Angle : 0.553 5.134 18595 Z= 0.339 Chirality : 0.033 0.131 2123 Planarity : 0.004 0.033 1341 Dihedral : 25.806 169.245 5540 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.32 % Allowed : 4.42 % Favored : 95.26 % 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: 2.43 (0.31), residues: 747 helix: 2.98 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.009 0.001 TYR C 50 ARG 0.003 0.000 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.10742 ( 719) hydrogen bonds : angle 3.10541 ( 1788) covalent geometry : bond 0.00351 (12837) covalent geometry : angle 0.55292 (18595) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.849 Fit side-chains REVERT: C 73 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7113 (t0) REVERT: C 75 LYS cc_start: 0.8483 (mmtp) cc_final: 0.8183 (mmtp) REVERT: C 99 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7910 (mtp85) REVERT: D 31 LYS cc_start: 0.8645 (mttm) cc_final: 0.8353 (mtmm) REVERT: D 59 MET cc_start: 0.9122 (mmp) cc_final: 0.8880 (mmm) REVERT: D 65 ASP cc_start: 0.9239 (t0) cc_final: 0.8871 (t0) REVERT: D 73 GLU cc_start: 0.9108 (tp30) cc_final: 0.8683 (tp30) REVERT: E 105 GLU cc_start: 0.8015 (tt0) cc_final: 0.7738 (mt-10) REVERT: F 74 GLU cc_start: 0.8251 (tt0) cc_final: 0.8015 (tt0) REVERT: G 73 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.6892 (t0) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 1.8816 time to fit residues: 236.0609 Evaluate side-chains 101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain G residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.069572 restraints weight = 20564.161| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.59 r_work: 0.2840 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12837 Z= 0.177 Angle : 0.534 5.095 18595 Z= 0.329 Chirality : 0.033 0.122 2123 Planarity : 0.004 0.036 1341 Dihedral : 28.966 168.495 4046 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.11 % Allowed : 9.64 % Favored : 89.26 % 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: 2.68 (0.31), residues: 747 helix: 3.15 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.72 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 31 PHE 0.012 0.002 PHE F 61 TYR 0.009 0.001 TYR G 50 ARG 0.005 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.06632 ( 719) hydrogen bonds : angle 2.51815 ( 1788) covalent geometry : bond 0.00371 (12837) covalent geometry : angle 0.53379 (18595) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.922 Fit side-chains REVERT: C 95 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8689 (ttpp) REVERT: C 99 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8108 (mtp85) REVERT: D 59 MET cc_start: 0.8858 (mmp) cc_final: 0.8626 (mmm) REVERT: D 65 ASP cc_start: 0.8994 (t0) cc_final: 0.8623 (t0) REVERT: D 73 GLU cc_start: 0.9029 (tp30) cc_final: 0.8628 (tp30) REVERT: E 105 GLU cc_start: 0.8089 (tt0) cc_final: 0.7713 (mt-10) REVERT: E 129 ARG cc_start: 0.8529 (tmt-80) cc_final: 0.8290 (tpt90) REVERT: F 74 GLU cc_start: 0.8424 (tt0) cc_final: 0.8174 (tt0) outliers start: 7 outliers final: 5 residues processed: 107 average time/residue: 1.9554 time to fit residues: 220.5282 Evaluate side-chains 107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.091465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069766 restraints weight = 20840.367| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.60 r_work: 0.2841 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12837 Z= 0.177 Angle : 0.531 5.372 18595 Z= 0.327 Chirality : 0.033 0.124 2123 Planarity : 0.004 0.037 1341 Dihedral : 28.978 168.568 4042 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.11 % Allowed : 10.58 % Favored : 88.31 % 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: 2.73 (0.31), residues: 747 helix: 3.19 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 106 PHE 0.011 0.002 PHE F 61 TYR 0.008 0.001 TYR G 50 ARG 0.007 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.06551 ( 719) hydrogen bonds : angle 2.47412 ( 1788) covalent geometry : bond 0.00373 (12837) covalent geometry : angle 0.53078 (18595) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.866 Fit side-chains REVERT: C 99 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8106 (mtp85) REVERT: D 59 MET cc_start: 0.8852 (mmp) cc_final: 0.8591 (mmm) REVERT: D 65 ASP cc_start: 0.8996 (t0) cc_final: 0.8559 (t0) REVERT: D 73 GLU cc_start: 0.9039 (tp30) cc_final: 0.8637 (tp30) REVERT: E 105 GLU cc_start: 0.8097 (tt0) cc_final: 0.7719 (mt-10) REVERT: F 74 GLU cc_start: 0.8431 (tt0) cc_final: 0.8183 (tt0) outliers start: 7 outliers final: 5 residues processed: 107 average time/residue: 1.9526 time to fit residues: 220.1851 Evaluate side-chains 105 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.064611 restraints weight = 20402.376| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.59 r_work: 0.2739 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 12837 Z= 0.294 Angle : 0.631 5.498 18595 Z= 0.382 Chirality : 0.039 0.153 2123 Planarity : 0.005 0.042 1341 Dihedral : 29.036 169.512 4042 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.05 % Allowed : 9.95 % 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: 2.24 (0.31), residues: 747 helix: 2.83 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 31 PHE 0.016 0.003 PHE F 61 TYR 0.011 0.002 TYR G 50 ARG 0.005 0.001 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.09559 ( 719) hydrogen bonds : angle 2.85845 ( 1788) covalent geometry : bond 0.00670 (12837) covalent geometry : angle 0.63087 (18595) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.926 Fit side-chains REVERT: C 73 ASN cc_start: 0.7550 (t0) cc_final: 0.6930 (t0) REVERT: C 74 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7923 (mtmm) REVERT: C 99 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8042 (mtp85) REVERT: D 65 ASP cc_start: 0.9099 (t0) cc_final: 0.8839 (t0) REVERT: D 73 GLU cc_start: 0.8991 (tp30) cc_final: 0.8426 (tp30) REVERT: D 82 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8875 (mtpt) REVERT: E 105 GLU cc_start: 0.8121 (tt0) cc_final: 0.7798 (mt-10) REVERT: F 74 GLU cc_start: 0.8614 (tt0) cc_final: 0.8331 (mt-10) REVERT: G 73 ASN cc_start: 0.7427 (t0) cc_final: 0.7001 (t0) outliers start: 13 outliers final: 8 residues processed: 112 average time/residue: 2.2682 time to fit residues: 267.6535 Evaluate side-chains 114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0770 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066560 restraints weight = 20529.299| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.60 r_work: 0.2773 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12837 Z= 0.182 Angle : 0.588 6.377 18595 Z= 0.357 Chirality : 0.034 0.125 2123 Planarity : 0.004 0.038 1341 Dihedral : 29.011 169.543 4042 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.26 % Allowed : 12.16 % Favored : 86.57 % 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: 2.24 (0.31), residues: 747 helix: 2.84 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.95 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 106 PHE 0.010 0.001 PHE B 61 TYR 0.009 0.001 TYR F 51 ARG 0.006 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.08053 ( 719) hydrogen bonds : angle 2.87183 ( 1788) covalent geometry : bond 0.00358 (12837) covalent geometry : angle 0.58770 (18595) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.850 Fit side-chains REVERT: C 73 ASN cc_start: 0.7485 (t0) cc_final: 0.6910 (t0) REVERT: C 99 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8035 (mtp85) REVERT: D 31 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8458 (mttp) REVERT: D 65 ASP cc_start: 0.9097 (t0) cc_final: 0.8767 (t0) REVERT: D 73 GLU cc_start: 0.8984 (tp30) cc_final: 0.8367 (tp30) REVERT: D 82 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8892 (mtpt) REVERT: F 74 GLU cc_start: 0.8534 (tt0) cc_final: 0.8267 (mt-10) REVERT: G 73 ASN cc_start: 0.7279 (t0) cc_final: 0.6849 (t0) outliers start: 8 outliers final: 5 residues processed: 107 average time/residue: 1.9287 time to fit residues: 217.8616 Evaluate side-chains 107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 40 optimal weight: 0.0060 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.065770 restraints weight = 21190.930| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.59 r_work: 0.2761 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12837 Z= 0.216 Angle : 0.571 5.229 18595 Z= 0.350 Chirality : 0.035 0.136 2123 Planarity : 0.005 0.040 1341 Dihedral : 28.972 168.686 4042 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.58 % Allowed : 12.16 % Favored : 86.26 % 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: 2.33 (0.31), residues: 747 helix: 2.94 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -2.01 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 106 PHE 0.012 0.002 PHE F 61 TYR 0.009 0.001 TYR G 50 ARG 0.008 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.07871 ( 719) hydrogen bonds : angle 2.66603 ( 1788) covalent geometry : bond 0.00471 (12837) covalent geometry : angle 0.57149 (18595) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.037 Fit side-chains REVERT: C 99 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8182 (mtp85) REVERT: D 65 ASP cc_start: 0.9181 (t0) cc_final: 0.8740 (t0) REVERT: D 73 GLU cc_start: 0.9068 (tp30) cc_final: 0.8474 (tp30) REVERT: D 82 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8945 (mtpt) REVERT: F 74 GLU cc_start: 0.8566 (tt0) cc_final: 0.8360 (tt0) REVERT: G 73 ASN cc_start: 0.7167 (t0) cc_final: 0.6794 (t0) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 2.1973 time to fit residues: 252.9261 Evaluate side-chains 111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.8576 > 50: distance: 108 - 110: 6.641 distance: 110 - 111: 11.089 distance: 111 - 112: 22.078 distance: 111 - 114: 5.153 distance: 112 - 113: 18.523 distance: 112 - 121: 18.804 distance: 114 - 115: 34.901 distance: 116 - 117: 5.122 distance: 117 - 118: 16.210 distance: 118 - 119: 16.200 distance: 118 - 120: 15.460 distance: 121 - 122: 8.680 distance: 122 - 123: 30.115 distance: 122 - 125: 12.201 distance: 123 - 124: 10.156 distance: 123 - 128: 10.615 distance: 125 - 126: 21.426 distance: 125 - 127: 8.876 distance: 128 - 129: 5.646 distance: 129 - 130: 12.293 distance: 129 - 132: 16.746 distance: 130 - 131: 10.509 distance: 130 - 135: 7.511 distance: 132 - 133: 10.454 distance: 132 - 134: 20.214 distance: 135 - 136: 7.317 distance: 136 - 137: 12.811 distance: 136 - 139: 17.417 distance: 137 - 138: 29.042 distance: 137 - 143: 16.664 distance: 139 - 140: 31.471 distance: 139 - 141: 25.083 distance: 140 - 142: 16.820 distance: 143 - 144: 17.349 distance: 144 - 145: 29.521 distance: 144 - 147: 25.476 distance: 145 - 146: 9.862 distance: 145 - 148: 13.769 distance: 148 - 149: 9.897 distance: 149 - 150: 16.083 distance: 149 - 152: 18.844 distance: 150 - 151: 24.567 distance: 150 - 157: 20.566 distance: 152 - 153: 26.623 distance: 153 - 154: 18.990 distance: 154 - 155: 23.414 distance: 154 - 156: 16.784 distance: 157 - 158: 36.964 distance: 158 - 159: 36.598 distance: 159 - 160: 25.373 distance: 159 - 161: 17.379 distance: 161 - 162: 17.575 distance: 162 - 163: 26.905 distance: 163 - 164: 21.584 distance: 163 - 165: 23.606 distance: 165 - 166: 6.254 distance: 166 - 167: 23.314 distance: 166 - 169: 11.939 distance: 167 - 168: 29.688 distance: 167 - 172: 28.702 distance: 169 - 170: 47.712 distance: 169 - 171: 35.773 distance: 172 - 173: 7.583 distance: 173 - 176: 19.109 distance: 174 - 180: 28.580 distance: 176 - 177: 37.859 distance: 177 - 178: 25.472 distance: 177 - 179: 25.708