Starting phenix.real_space_refine on Fri Jun 28 09:19:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.pdb" } resolution = 4.1 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5073 atoms to isotropic. 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 S 23 5.16 5 C 3168 2.51 5 N 854 2.21 5 O 1051 1.98 5 H 4901 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 10": Residue "C PHE 10": Residue "C ASP 17": "OD1" <-> "OD2" Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9997 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4485 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 4416 Classifications: {'peptide': 282} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 282, 4416 Classifications: {'peptide': 282} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 bond proxies already assigned to first conformer: 4386 Chain: "B" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1058 Chain: "C" Number of atoms: 1105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1035 Chain: "D" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1054 Classifications: {'peptide': 69} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Chain: "E" Number of atoms: 1079 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1067 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1067 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1064 Chain: "F" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1067 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1068 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1061 Chain: "P" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ASER A 99 " occ=0.38 ... (20 atoms not shown) pdb=" HG BSER A 99 " occ=0.62 residue: pdb=" N AARG A 119 " occ=0.59 ... (46 atoms not shown) pdb="HH22BARG A 119 " occ=0.41 residue: pdb=" N ASER A 278 " occ=0.27 ... (20 atoms not shown) pdb=" HG BSER A 278 " occ=0.73 residue: pdb=" N AVAL B 65 " occ=0.74 ... (30 atoms not shown) pdb="HG23BVAL B 65 " occ=0.26 residue: pdb=" N AGLU C 9 " occ=0.47 ... (28 atoms not shown) pdb=" HG3BGLU C 9 " occ=0.53 residue: pdb=" N ASER C 60 " occ=0.61 ... (20 atoms not shown) pdb=" HG BSER C 60 " occ=0.39 residue: pdb=" N ASER E 60 " occ=0.38 ... (20 atoms not shown) pdb=" HG BSER E 60 " occ=0.62 residue: pdb=" N ACYS F 3 " occ=0.68 ... (19 atoms not shown) pdb=" HG BCYS F 3 " occ=0.32 Time building chain proxies: 8.17, per 1000 atoms: 0.82 Number of scatterers: 9997 At special positions: 0 Unit cell: (78.356, 97.3264, 109.698, 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 23 16.00 O 1051 8.00 N 854 7.00 C 3168 6.00 H 4901 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 56 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 56 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 56 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 56 " distance=2.03 Simple disulfide: pdb=" SG ACYS F 3 " - pdb=" SG CYS F 56 " distance=2.04 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: 8.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 13 sheets defined 28.9% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'A' and resid 151 through 164 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 171 through 179 removed outlier: 4.366A pdb=" N GLN A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 227 through 235 removed outlier: 4.042A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 removed outlier: 4.079A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.600A pdb=" N TYR A 293 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.940A pdb=" N LEU B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 45 removed outlier: 4.522A pdb=" N LEU C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.695A pdb=" N LEU D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 45 Processing helix chain 'F' and resid 34 through 46 removed outlier: 4.578A pdb=" N LEU F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN F 40 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 5.105A pdb=" N LEU A 67 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU A 72 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 78 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.570A pdb=" N TYR A 189 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 225 removed outlier: 6.849A pdb=" N GLY A 217 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLU A 277 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ARG A 219 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 6 removed outlier: 6.485A pdb=" N ILE B 51 " --> pdb=" O CYS B 3 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS B 5 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 49 " --> pdb=" O LYS B 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 14 Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.944A pdb=" N PHE C 10 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU C 64 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.667A pdb=" N GLU D 64 " --> pdb=" O LYS D 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 14 removed outlier: 3.742A pdb=" N THR D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.614A pdb=" N PHE E 10 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 23 " --> pdb=" O LYS E 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 4 through 6 removed outlier: 4.213A pdb=" N ALA F 4 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 13 removed outlier: 4.439A pdb=" N PHE F 10 " --> pdb=" O LYS F 22 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4900 1.03 - 1.23: 25 1.23 - 1.43: 2212 1.43 - 1.62: 2904 1.62 - 1.82: 33 Bond restraints: 10074 Sorted by residual: bond pdb=" C SER A 37 " pdb=" N VAL A 38 " ideal model delta sigma weight residual 1.335 1.325 0.010 1.41e-02 5.03e+03 5.00e-01 bond pdb=" N THR C 20 " pdb=" CA THR C 20 " ideal model delta sigma weight residual 1.463 1.454 0.009 1.28e-02 6.10e+03 4.60e-01 bond pdb=" CA VAL C 21 " pdb=" C VAL C 21 " ideal model delta sigma weight residual 1.526 1.520 0.006 1.04e-02 9.25e+03 3.69e-01 bond pdb=" CA VAL A 38 " pdb=" CB VAL A 38 " ideal model delta sigma weight residual 1.538 1.544 -0.007 1.10e-02 8.26e+03 3.50e-01 bond pdb=" CA GLU C 64 " pdb=" C GLU C 64 " ideal model delta sigma weight residual 1.529 1.523 0.006 1.04e-02 9.25e+03 3.43e-01 ... (remaining 10069 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.67: 50 105.67 - 112.75: 11412 112.75 - 119.83: 2660 119.83 - 126.91: 3909 126.91 - 133.99: 53 Bond angle restraints: 18084 Sorted by residual: angle pdb=" CB ARG A 156 " pdb=" CG ARG A 156 " pdb=" CD ARG A 156 " ideal model delta sigma weight residual 111.30 117.77 -6.47 2.30e+00 1.89e-01 7.91e+00 angle pdb=" CB ARG A 21 " pdb=" CG ARG A 21 " pdb=" CD ARG A 21 " ideal model delta sigma weight residual 111.30 117.34 -6.04 2.30e+00 1.89e-01 6.89e+00 angle pdb=" N VAL C 21 " pdb=" CA VAL C 21 " pdb=" C VAL C 21 " ideal model delta sigma weight residual 110.05 107.66 2.39 1.09e+00 8.42e-01 4.79e+00 angle pdb=" N VAL A 38 " pdb=" CA VAL A 38 " pdb=" C VAL A 38 " ideal model delta sigma weight residual 110.21 107.80 2.41 1.13e+00 7.83e-01 4.56e+00 angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " ideal model delta sigma weight residual 110.12 113.12 -3.00 1.47e+00 4.63e-01 4.15e+00 ... (remaining 18079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4365 17.97 - 35.94: 329 35.94 - 53.91: 73 53.91 - 71.88: 20 71.88 - 89.85: 5 Dihedral angle restraints: 4792 sinusoidal: 2567 harmonic: 2225 Sorted by residual: dihedral pdb=" CB CYS E 3 " pdb=" SG CYS E 3 " pdb=" SG CYS E 56 " pdb=" CB CYS E 56 " ideal model delta sinusoidal sigma weight residual -86.00 -56.34 -29.66 1 1.00e+01 1.00e-02 1.26e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 56 " pdb=" CB CYS C 56 " ideal model delta sinusoidal sigma weight residual -86.00 -57.64 -28.36 1 1.00e+01 1.00e-02 1.15e+01 dihedral pdb=" CA CYS D 3 " pdb=" CB CYS D 3 " pdb=" SG CYS D 3 " pdb=" SG CYS D 56 " ideal model delta sinusoidal sigma weight residual 79.00 22.66 56.34 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 482 0.028 - 0.056: 202 0.056 - 0.085: 41 0.085 - 0.113: 48 0.113 - 0.141: 14 Chirality restraints: 787 Sorted by residual: chirality pdb=" CA VAL C 65 " pdb=" N VAL C 65 " pdb=" C VAL C 65 " pdb=" CB VAL C 65 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE D 51 " pdb=" N ILE D 51 " pdb=" C ILE D 51 " pdb=" CB ILE D 51 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 784 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 209 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 210 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.010 9.50e-02 1.11e+02 6.87e-03 8.19e-01 pdb=" NE ARG A 156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " 0.003 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 36 " -0.005 2.00e-02 2.50e+03 8.94e-03 7.99e-01 pdb=" C GLN E 36 " 0.015 2.00e-02 2.50e+03 pdb=" O GLN E 36 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO E 37 " -0.005 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 562 2.15 - 2.76: 20224 2.76 - 3.37: 29497 3.37 - 3.99: 37774 3.99 - 4.60: 57473 Nonbonded interactions: 145530 Sorted by model distance: nonbonded pdb=" OE2 GLU A 72 " pdb=" H TYR A 77 " model vdw 1.531 1.850 nonbonded pdb=" H HIS A 66 " pdb=" OH TYR A 139 " model vdw 1.550 1.850 nonbonded pdb=" OD1 ASP E 16 " pdb=" HG1 THR E 18 " model vdw 1.572 1.850 nonbonded pdb=" O ILE A 54 " pdb="HH11 ARG A 55 " model vdw 1.584 1.850 nonbonded pdb=" OD1 ASN C 14 " pdb=" H GLU C 15 " model vdw 1.591 1.850 ... (remaining 145525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 70)) selection = (chain 'C' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 70)) selection = (chain 'D' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 59 or resid 62 t \ hrough 64 or resid 67 through 70)) selection = (chain 'E' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA or \ name HB2 or name HB3)))) selection = (chain 'F' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA or \ name HB2 or name HB3)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.12 max=1.00 mean=0.98 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.190 Extract box with map and model: 5.710 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 39.200 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3344 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 : 0.002 0.016 5173 Z= 0.146 Angle : 0.524 6.467 7012 Z= 0.315 Chirality : 0.041 0.141 787 Planarity : 0.002 0.037 908 Dihedral : 13.786 88.086 1861 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.57 % Allowed : 0.52 % Favored : 97.90 % 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: -0.16 (0.34), residues: 643 helix: 1.06 (0.47), residues: 159 sheet: -0.12 (0.42), residues: 150 loop : -0.62 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 33 HIS 0.004 0.001 HIS A 66 PHE 0.009 0.001 PHE A 81 TYR 0.013 0.001 TYR A 139 ARG 0.013 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.850 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 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 revert: symmetry clash REVERT: A 108 MET cc_start: 0.0664 (tpp) cc_final: 0.0400 (tpp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3320 time to fit residues: 42.9959 Evaluate side-chains 84 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2705 > 50: distance: 118 - 146: 9.726 distance: 133 - 146: 9.738 distance: 146 - 147: 11.981 distance: 146 - 166: 3.118 distance: 147 - 148: 17.601 distance: 147 - 150: 14.918 distance: 147 - 157: 10.407 distance: 148 - 149: 13.290 distance: 148 - 167: 11.864 distance: 149 - 336: 22.799 distance: 150 - 151: 15.606 distance: 150 - 158: 14.033 distance: 151 - 152: 19.045 distance: 151 - 153: 6.324 distance: 152 - 154: 11.706 distance: 152 - 160: 12.333 distance: 153 - 155: 23.442 distance: 153 - 161: 8.644 distance: 154 - 156: 22.524 distance: 154 - 162: 13.670 distance: 155 - 156: 17.647 distance: 155 - 163: 3.852 distance: 156 - 164: 6.114 distance: 167 - 168: 11.399 distance: 167 - 173: 25.093 distance: 168 - 169: 19.602 distance: 168 - 171: 27.663 distance: 168 - 174: 31.827 distance: 169 - 170: 10.211 distance: 169 - 178: 20.607 distance: 171 - 172: 18.660 distance: 171 - 175: 37.365 distance: 171 - 176: 29.134 distance: 172 - 177: 53.754 distance: 178 - 179: 20.228 distance: 178 - 187: 17.445 distance: 178 - 311: 30.235 distance: 179 - 180: 3.671 distance: 179 - 182: 12.424 distance: 179 - 188: 20.246 distance: 180 - 181: 25.342 distance: 180 - 200: 21.077 distance: 181 - 308: 26.028 distance: 182 - 183: 13.125 distance: 182 - 189: 16.611 distance: 182 - 190: 11.718 distance: 183 - 184: 16.183 distance: 183 - 192: 4.426 distance: 184 - 185: 4.289 distance: 184 - 193: 13.363 distance: 184 - 194: 10.736 distance: 185 - 186: 7.527 distance: 185 - 195: 5.864 distance: 185 - 196: 10.450 distance: 186 - 197: 9.647 distance: 186 - 198: 14.339 distance: 186 - 199: 13.692 distance: 200 - 212: 4.661 distance: 201 - 202: 6.740 distance: 201 - 204: 4.165 distance: 201 - 213: 7.182 distance: 204 - 205: 8.555 distance: 204 - 214: 11.976 distance: 204 - 215: 19.301 distance: 205 - 206: 6.842 distance: 205 - 207: 4.486 distance: 206 - 208: 9.758 distance: 206 - 216: 4.759 distance: 207 - 209: 11.888 distance: 208 - 210: 12.411 distance: 208 - 218: 18.501 distance: 209 - 210: 7.944 distance: 210 - 211: 12.128 distance: 211 - 220: 23.989 distance: 221 - 229: 12.708 distance: 222 - 223: 13.054 distance: 222 - 225: 40.101 distance: 222 - 230: 5.128 distance: 223 - 224: 28.587 distance: 223 - 235: 19.585 distance: 225 - 226: 8.676 distance: 225 - 231: 12.896 distance: 225 - 232: 13.060 distance: 226 - 227: 20.601 distance: 226 - 228: 27.287 distance: 228 - 233: 12.790 distance: 235 - 236: 35.708 distance: 235 - 244: 24.892 distance: 236 - 237: 16.051 distance: 236 - 239: 18.840 distance: 236 - 245: 17.542 distance: 237 - 238: 3.741 distance: 237 - 250: 16.140 distance: 239 - 240: 18.177 distance: 239 - 246: 12.556 distance: 239 - 247: 11.005 distance: 240 - 241: 18.629 distance: 240 - 248: 17.897 distance: 240 - 249: 29.277 distance: 241 - 242: 21.850 distance: 241 - 243: 30.564 distance: 250 - 251: 10.666 distance: 250 - 258: 15.053 distance: 251 - 252: 14.776 distance: 251 - 254: 26.177 distance: 251 - 259: 36.067 distance: 252 - 253: 23.025 distance: 252 - 262: 18.087 distance: 254 - 255: 29.583 distance: 254 - 260: 20.024 distance: 254 - 261: 30.891 distance: 255 - 256: 24.816 distance: 255 - 257: 36.892 distance: 262 - 263: 17.458 distance: 262 - 270: 17.862 distance: 263 - 264: 11.050 distance: 263 - 266: 23.877 distance: 263 - 271: 16.862 distance: 264 - 265: 4.440 distance: 264 - 274: 13.985 distance: 266 - 267: 36.392 distance: 266 - 272: 29.027 distance: 266 - 273: 14.071 distance: 267 - 268: 21.632 distance: 267 - 269: 24.642 distance: 274 - 275: 4.086 distance: 274 - 281: 6.650 distance: 275 - 276: 21.214 distance: 275 - 278: 37.032 distance: 275 - 282: 30.138 distance: 276 - 277: 12.427 distance: 276 - 288: 21.007 distance: 278 - 279: 7.557 distance: 278 - 280: 29.446 distance: 278 - 283: 3.717 distance: 279 - 284: 51.587 distance: 280 - 285: 28.412 distance: 280 - 286: 10.424 distance: 280 - 287: 4.952 distance: 288 - 289: 21.043 distance: 288 - 299: 32.773 distance: 288 - 375: 26.201 distance: 289 - 290: 40.060 distance: 289 - 292: 5.795 distance: 289 - 300: 16.119 distance: 290 - 291: 19.707 distance: 290 - 308: 25.380 distance: 291 - 372: 11.154 distance: 292 - 293: 15.575 distance: 292 - 301: 27.833 distance: 292 - 302: 8.318 distance: 293 - 294: 24.905 distance: 293 - 295: 20.490 distance: 294 - 296: 19.471 distance: 294 - 303: 16.142 distance: 295 - 297: 13.528 distance: 295 - 304: 4.472 distance: 296 - 298: 27.972 distance: 296 - 305: 7.633 distance: 297 - 298: 13.258 distance: 297 - 306: 10.320 distance: 298 - 307: 25.613