Starting phenix.real_space_refine on Sun Dec 10 07:24:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/12_2023/7dbp_30161.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/12_2023/7dbp_30161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/12_2023/7dbp_30161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/12_2023/7dbp_30161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/12_2023/7dbp_30161.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/12_2023/7dbp_30161.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 350 5.49 5 S 15 5.16 5 C 7571 2.51 5 N 2590 2.21 5 O 3275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 22": "NH1" <-> "NH2" Residue "K ARG 27": "NH1" <-> "NH2" Residue "K TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13801 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 590 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 3569 Classifications: {'DNA': 175} Link IDs: {'rna3p': 174} Chain: "J" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 3606 Classifications: {'DNA': 175} Link IDs: {'rna3p': 174} Time building chain proxies: 7.55, per 1000 atoms: 0.55 Number of scatterers: 13801 At special positions: 0 Unit cell: (123.2, 88, 160.6, 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 15 16.00 P 350 15.00 O 3275 8.00 N 2590 7.00 C 7571 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: 7.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1558 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 68.8% alpha, 2.4% beta 36 base pairs and 212 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'K' and resid 7 through 19 Processing helix chain 'K' and resid 27 through 38 Processing helix chain 'K' and resid 41 through 46 Processing helix chain 'K' and resid 46 through 59 removed outlier: 4.586A pdb=" N LEU K 50 " --> pdb=" O SER K 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.824A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.682A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.517A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.528A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.841A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.566A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.897A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.519A 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 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.557A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.517A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.570A pdb=" N MET D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.835A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.824A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.680A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.517A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.528A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.841A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.567A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.898A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.557A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.518A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.570A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.835A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 25 through 26 removed outlier: 3.501A pdb=" N SER K 25 " --> pdb=" O PHE K 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.432A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.535A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.081A 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 'G' and resid 42 through 43 removed outlier: 7.727A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.519A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 404 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 212 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 7.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2627 1.33 - 1.45: 4905 1.45 - 1.57: 6504 1.57 - 1.69: 698 1.69 - 1.81: 26 Bond restraints: 14760 Sorted by residual: bond pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" C3' DT J -81 " pdb=" O3' DT J -81 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" C3' DT I -38 " pdb=" O3' DT I -38 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" C3' DT I 54 " pdb=" O3' DT I 54 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" C3' DC J 54 " pdb=" O3' DC J 54 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.08e+00 ... (remaining 14755 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.14: 2165 106.14 - 112.72: 7818 112.72 - 119.31: 3856 119.31 - 125.89: 6430 125.89 - 132.48: 1160 Bond angle restraints: 21429 Sorted by residual: angle pdb=" C TYR B 98 " pdb=" CA TYR B 98 " pdb=" CB TYR B 98 " ideal model delta sigma weight residual 114.16 108.43 5.73 2.31e+00 1.87e-01 6.16e+00 angle pdb=" C TYR F 98 " pdb=" CA TYR F 98 " pdb=" CB TYR F 98 " ideal model delta sigma weight residual 114.16 108.48 5.68 2.31e+00 1.87e-01 6.04e+00 angle pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 123.38 -3.18 1.50e+00 4.44e-01 4.50e+00 angle pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" C TYR F 98 " ideal model delta sigma weight residual 109.31 112.16 -2.85 1.42e+00 4.96e-01 4.04e+00 angle pdb=" N TYR B 98 " pdb=" CA TYR B 98 " pdb=" C TYR B 98 " ideal model delta sigma weight residual 109.31 112.15 -2.84 1.42e+00 4.96e-01 4.01e+00 ... (remaining 21424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 6501 35.47 - 70.94: 1431 70.94 - 106.42: 32 106.42 - 141.89: 6 141.89 - 177.36: 3 Dihedral angle restraints: 7973 sinusoidal: 5554 harmonic: 2419 Sorted by residual: dihedral pdb=" C4' DT J -81 " pdb=" C3' DT J -81 " pdb=" O3' DT J -81 " pdb=" P DA J -80 " ideal model delta sinusoidal sigma weight residual -140.00 37.36 -177.36 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I 54 " pdb=" C3' DT I 54 " pdb=" O3' DT I 54 " pdb=" P DG I 55 " ideal model delta sinusoidal sigma weight residual -140.00 36.20 -176.20 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 51.88 168.12 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 7970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1672 0.024 - 0.048: 553 0.048 - 0.072: 147 0.072 - 0.096: 28 0.096 - 0.120: 34 Chirality restraints: 2434 Sorted by residual: chirality pdb=" CA ILE D 86 " pdb=" N ILE D 86 " pdb=" C ILE D 86 " pdb=" CB ILE D 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE H 86 " pdb=" N ILE H 86 " pdb=" C ILE H 86 " pdb=" CB ILE H 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-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 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 2431 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I -74 " 0.018 2.00e-02 2.50e+03 9.01e-03 1.83e+00 pdb=" N1 DC I -74 " -0.016 2.00e-02 2.50e+03 pdb=" C2 DC I -74 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I -74 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DC I -74 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC I -74 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC I -74 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I -74 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC I -74 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 81 " -0.018 2.00e-02 2.50e+03 7.95e-03 1.74e+00 pdb=" N9 DA I 81 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 81 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 81 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 81 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 81 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 81 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 81 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 81 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 81 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 81 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 60 " -0.017 2.00e-02 2.50e+03 7.71e-03 1.63e+00 pdb=" N9 DA I 60 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 60 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 60 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 60 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 60 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 60 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA I 60 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 60 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 60 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 60 " 0.003 2.00e-02 2.50e+03 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1767 2.76 - 3.30: 12189 3.30 - 3.83: 24588 3.83 - 4.37: 27978 4.37 - 4.90: 41372 Nonbonded interactions: 107894 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OP1 DC J 70 " model vdw 2.226 2.440 nonbonded pdb=" N2 DG I 26 " pdb=" O2 DT J -25 " model vdw 2.294 2.520 nonbonded pdb=" N2 DG J 76 " pdb=" O6 DG J 77 " model vdw 2.306 2.520 nonbonded pdb=" O LEU D 77 " pdb=" ND2 ASN D 81 " model vdw 2.320 2.520 nonbonded pdb=" O LEU H 77 " pdb=" ND2 ASN H 81 " model vdw 2.320 2.520 ... (remaining 107889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } 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 group one per residue 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: 0.710 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: 0.000 Extract box with map and model: 3.710 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 40.720 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 0.040 14760 Z= 0.137 Angle : 0.451 5.734 21429 Z= 0.291 Chirality : 0.028 0.120 2434 Planarity : 0.003 0.026 1497 Dihedral : 27.262 177.360 6415 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.40 % Favored : 94.87 % Rotamer: Outliers : 0.57 % Allowed : 2.15 % Favored : 97.28 % 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: -0.94 (0.27), residues: 819 helix: 0.21 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -2.58 (0.30), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 113 PHE 0.007 0.001 PHE D 62 TYR 0.010 0.001 TYR C 50 ARG 0.002 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 210 average time/residue: 0.3862 time to fit residues: 104.6782 Evaluate side-chains 65 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1436 time to fit residues: 1.6973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 HIS K 17 GLN K 31 GLN K 37 HIS A 68 GLN A 76 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 93 GLN G 31 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 14760 Z= 0.441 Angle : 0.795 10.366 21429 Z= 0.461 Chirality : 0.043 0.200 2434 Planarity : 0.006 0.066 1497 Dihedral : 32.161 172.628 4757 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.69 % Favored : 97.19 % Rotamer: Outliers : 0.57 % Allowed : 2.87 % Favored : 96.56 % 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: 0.07 (0.28), residues: 819 helix: 0.99 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.32 (0.31), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 75 PHE 0.025 0.003 PHE B 61 TYR 0.024 0.002 TYR H 37 ARG 0.011 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 82 average time/residue: 0.3593 time to fit residues: 39.6669 Evaluate side-chains 44 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 69.2012 > 50: distance: 60 - 64: 35.021 distance: 64 - 65: 53.825 distance: 65 - 66: 8.589 distance: 66 - 67: 25.474 distance: 66 - 68: 28.084 distance: 68 - 69: 43.732 distance: 69 - 70: 41.930 distance: 70 - 71: 40.255 distance: 72 - 73: 27.412 distance: 73 - 74: 49.884 distance: 73 - 76: 28.925 distance: 74 - 75: 15.200 distance: 74 - 79: 14.487 distance: 76 - 77: 25.228 distance: 76 - 78: 23.682 distance: 79 - 80: 20.826 distance: 80 - 81: 28.565 distance: 80 - 83: 39.310 distance: 81 - 82: 9.479 distance: 81 - 87: 31.439 distance: 83 - 84: 19.034 distance: 84 - 85: 38.597 distance: 84 - 86: 22.473 distance: 87 - 88: 22.483 distance: 87 - 93: 44.047 distance: 88 - 89: 28.224 distance: 88 - 91: 49.805 distance: 89 - 90: 11.978 distance: 89 - 94: 29.387 distance: 91 - 92: 21.728 distance: 92 - 93: 40.656 distance: 94 - 95: 8.323 distance: 95 - 96: 62.326 distance: 95 - 98: 31.709 distance: 96 - 102: 54.372 distance: 98 - 99: 10.338 distance: 99 - 100: 14.524 distance: 99 - 101: 17.608 distance: 102 - 103: 34.873 distance: 103 - 104: 36.481 distance: 103 - 106: 39.665 distance: 104 - 105: 23.945 distance: 104 - 110: 55.965 distance: 106 - 107: 42.215 distance: 106 - 108: 4.974 distance: 107 - 109: 20.277 distance: 110 - 111: 4.365 distance: 111 - 112: 44.456 distance: 111 - 114: 23.108 distance: 112 - 113: 32.062 distance: 112 - 119: 57.604 distance: 115 - 116: 46.698 distance: 116 - 117: 6.916 distance: 116 - 118: 39.024 distance: 119 - 120: 31.883 distance: 120 - 121: 19.048 distance: 120 - 123: 25.837 distance: 121 - 124: 40.469 distance: 124 - 125: 40.036 distance: 125 - 126: 11.264 distance: 125 - 128: 33.706 distance: 126 - 127: 22.883 distance: 126 - 131: 23.206 distance: 128 - 129: 36.232 distance: 128 - 130: 37.735