Starting phenix.real_space_refine on Thu Dec 7 19:34:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/12_2023/7efd_31084.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/12_2023/7efd_31084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/12_2023/7efd_31084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/12_2023/7efd_31084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/12_2023/7efd_31084.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/12_2023/7efd_31084.pdb" } resolution = 1.77 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= 0.007 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: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 2392 2.51 5 N 668 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "C TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4004 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 951 Unusual residues: {'BTN': 1} Classifications: {'peptide': 120, 'undetermined': 1, 'water': 39} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 40} Not linked: pdbres="LYS A 134 " pdbres="BTN A5100 " Not linked: pdbres="BTN A5100 " pdbres="HOH A5201 " Not linked: pdbres="HOH A5201 " pdbres="HOH A5202 " Not linked: pdbres="HOH A5202 " pdbres="HOH A5203 " Not linked: pdbres="HOH A5203 " pdbres="HOH A5204 " ... (remaining 35 not shown) Conformer: "B" Number of residues, atoms: 155, 931 Classifications: {'peptide': 120, 'water': 35} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 35} Not linked: pdbres="LYS A 134 " pdbres="HOH A5201 " Not linked: pdbres="HOH A5201 " pdbres="HOH A5202 " Not linked: pdbres="HOH A5202 " pdbres="HOH A5203 " Not linked: pdbres="HOH A5203 " pdbres="HOH A5204 " Not linked: pdbres="HOH A5204 " pdbres="HOH A5205 " ... (remaining 30 not shown) bond proxies already assigned to first conformer: 867 Chain: "B" Number of atoms: 1001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 951 Unusual residues: {'BTN': 1} Classifications: {'peptide': 120, 'undetermined': 1, 'water': 39} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 40} Not linked: pdbres="LYS B 134 " pdbres="BTN B5100 " Not linked: pdbres="BTN B5100 " pdbres="HOH B5201 " Not linked: pdbres="HOH B5201 " pdbres="HOH B5202 " Not linked: pdbres="HOH B5202 " pdbres="HOH B5203 " Not linked: pdbres="HOH B5203 " pdbres="HOH B5204 " ... (remaining 35 not shown) Conformer: "B" Number of residues, atoms: 155, 931 Classifications: {'peptide': 120, 'water': 35} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 35} Not linked: pdbres="LYS B 134 " pdbres="HOH B5201 " Not linked: pdbres="HOH B5201 " pdbres="HOH B5202 " Not linked: pdbres="HOH B5202 " pdbres="HOH B5203 " Not linked: pdbres="HOH B5203 " pdbres="HOH B5204 " Not linked: pdbres="HOH B5204 " pdbres="HOH B5205 " ... (remaining 30 not shown) bond proxies already assigned to first conformer: 867 Chain: "C" Number of atoms: 1001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 951 Unusual residues: {'BTN': 1} Classifications: {'peptide': 120, 'undetermined': 1, 'water': 39} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 40} Not linked: pdbres="LYS C 134 " pdbres="BTN C5100 " Not linked: pdbres="BTN C5100 " pdbres="HOH C5201 " Not linked: pdbres="HOH C5201 " pdbres="HOH C5202 " Not linked: pdbres="HOH C5202 " pdbres="HOH C5203 " Not linked: pdbres="HOH C5203 " pdbres="HOH C5204 " ... (remaining 35 not shown) Conformer: "B" Number of residues, atoms: 155, 931 Classifications: {'peptide': 120, 'water': 35} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 35} Not linked: pdbres="LYS C 134 " pdbres="HOH C5201 " Not linked: pdbres="HOH C5201 " pdbres="HOH C5202 " Not linked: pdbres="HOH C5202 " pdbres="HOH C5203 " Not linked: pdbres="HOH C5203 " pdbres="HOH C5204 " Not linked: pdbres="HOH C5204 " pdbres="HOH C5205 " ... (remaining 30 not shown) bond proxies already assigned to first conformer: 867 Chain: "D" Number of atoms: 1001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 951 Unusual residues: {'BTN': 1} Classifications: {'peptide': 120, 'undetermined': 1, 'water': 39} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 40} Not linked: pdbres="LYS D 134 " pdbres="BTN D5100 " Not linked: pdbres="BTN D5100 " pdbres="HOH D5201 " Not linked: pdbres="HOH D5201 " pdbres="HOH D5202 " Not linked: pdbres="HOH D5202 " pdbres="HOH D5203 " Not linked: pdbres="HOH D5203 " pdbres="HOH D5204 " ... (remaining 35 not shown) Conformer: "B" Number of residues, atoms: 155, 931 Classifications: {'peptide': 120, 'water': 35} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 35} Not linked: pdbres="LYS D 134 " pdbres="HOH D5201 " Not linked: pdbres="HOH D5201 " pdbres="HOH D5202 " Not linked: pdbres="HOH D5202 " pdbres="HOH D5203 " Not linked: pdbres="HOH D5203 " pdbres="HOH D5204 " Not linked: pdbres="HOH D5204 " pdbres="HOH D5205 " ... (remaining 30 not shown) bond proxies already assigned to first conformer: 867 Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ASER A 45 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 45 " occ=0.50 residue: pdb=" N AALA A 46 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 46 " occ=0.50 residue: pdb=" N AVAL A 47 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 47 " occ=0.50 residue: pdb=" N AGLY A 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.50 residue: pdb=" N AASN A 49 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 49 " occ=0.50 residue: pdb=" N AALA A 50 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 50 " occ=0.50 residue: pdb=" N AGLU A 51 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 51 " occ=0.50 residue: pdb=" N ASER A 52 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 52 " occ=0.50 residue: pdb=" C10ABTN A5100 " occ=0.50 ... (14 atoms not shown) pdb=" S1 ABTN A5100 " occ=0.50 residue: pdb=" O HOH A5223 " occ=0.50 residue: pdb=" O AHOH A5225 " occ=0.50 residue: pdb=" O AHOH A5226 " occ=0.50 ... (remaining 44 not shown) Time building chain proxies: 4.66, per 1000 atoms: 1.16 Number of scatterers: 4004 At special positions: 0 Unit cell: (68.8516, 64.4096, 58.4869, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 4 16.00 O 940 8.00 N 668 7.00 C 2392 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: 2.45 Conformation dependent library (CDL) restraints added in 2.1 seconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 5.8% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP C 120 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP D 120 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG A 53 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 80 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG B 53 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS B 80 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG C 53 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS C 80 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG D 53 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS D 80 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 540 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: 1.61 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 540 1.28 - 1.42: 876 1.42 - 1.55: 2196 1.55 - 1.68: 324 1.68 - 1.82: 8 Bond restraints: 3944 Sorted by residual: bond pdb=" C THR A 42 " pdb=" O THR A 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR B 42 " pdb=" O THR B 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR D 42 " pdb=" O THR D 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR C 42 " pdb=" O THR C 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 1.232 1.313 -0.082 1.05e-02 9.07e+03 6.03e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 94.81 - 103.65: 52 103.65 - 112.49: 1516 112.49 - 121.33: 2412 121.33 - 130.17: 1340 130.17 - 139.02: 80 Bond angle restraints: 5400 Sorted by residual: angle pdb=" CA PHE A 29 " pdb=" CB PHE A 29 " pdb=" CG PHE A 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE C 29 " pdb=" CB PHE C 29 " pdb=" CG PHE C 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " pdb=" CG PHE B 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE D 29 " pdb=" CB PHE D 29 " pdb=" CG PHE D 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA ILE A 17 " pdb=" C ILE A 17 " pdb=" O ILE A 17 " ideal model delta sigma weight residual 120.85 110.32 10.53 1.06e+00 8.90e-01 9.87e+01 ... (remaining 5395 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.60: 2012 16.60 - 33.19: 148 33.19 - 49.79: 28 49.79 - 66.38: 12 66.38 - 82.98: 12 Dihedral angle restraints: 2212 sinusoidal: 788 harmonic: 1424 Sorted by residual: dihedral pdb=" CA ASER C 52 " pdb=" C ASER C 52 " pdb=" N ARG C 53 " pdb=" CA ARG C 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER B 52 " pdb=" C ASER B 52 " pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER D 52 " pdb=" C ASER D 52 " pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 2209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 424 0.083 - 0.166: 152 0.166 - 0.248: 20 0.248 - 0.331: 0 0.331 - 0.414: 8 Chirality restraints: 604 Sorted by residual: chirality pdb=" CB VAL D 125 " pdb=" CA VAL D 125 " pdb=" CG1 VAL D 125 " pdb=" CG2 VAL D 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL C 125 " pdb=" CA VAL C 125 " pdb=" CG1 VAL C 125 " pdb=" CG2 VAL C 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 601 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 ABTN D5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN D5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN D5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN D5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN D5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN D5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN B5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN B5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN B5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN B5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN B5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN B5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN A5100 " -0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN A5100 " 0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN A5100 " 0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN A5100 " -0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN A5100 " -0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN A5100 " 0.245 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 2 0.98 - 1.96: 0 1.96 - 2.94: 1410 2.94 - 3.92: 11570 3.92 - 4.90: 22800 Warning: very small nonbonded interaction distances. Nonbonded interactions: 35782 Sorted by model distance: nonbonded pdb=" O HOH A5223 " pdb=" O HOH C5223 " model vdw 0.001 2.440 nonbonded pdb=" O HOH B5223 " pdb=" O HOH D5223 " model vdw 0.001 2.440 nonbonded pdb=" O AASN A 49 " pdb=" OD1AASN A 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN B 49 " pdb=" OD1AASN B 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN D 49 " pdb=" OD1AASN D 49 " model vdw 2.212 3.040 ... (remaining 35777 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 15 through 44 or resid 53 through 134)) selection = (chain 'B' and (resid 15 through 44 or resid 53 through 134)) selection = (chain 'C' and (resid 15 through 44 or resid 53 through 134)) selection = (chain 'D' and (resid 15 through 44 or resid 53 through 134)) } 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=0.50 max=1.00 mean=0.94 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: 0.140 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: 0.940 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.500 Find NCS groups from input model: 0.320 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.033 0.119 3944 Z= 2.153 Angle : 3.163 13.767 5400 Z= 2.200 Chirality : 0.091 0.414 604 Planarity : 0.015 0.201 684 Dihedral : 15.318 82.977 1324 Min Nonbonded Distance : 0.001 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.85 % Allowed : 1.69 % Favored : 97.46 % Rotamer: Outliers : 2.15 % Allowed : 4.30 % Favored : 93.55 % Cbeta Deviations : 2.70 % 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: -0.54 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.53 (0.31), residues: 224 loop : -1.12 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 92 HIS 0.001 0.000 HIS B 127 PHE 0.002 0.001 PHE C 130 TYR 0.002 0.001 TYR D 60 ARG 0.000 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 1.4085 time to fit residues: 92.8035 Evaluate side-chains 60 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0401 time to fit residues: 0.7950 ------------------------------------------------------------------------------- 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-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: 64.0343 > 50: distance: 22 - 48: 35.621 distance: 25 - 45: 15.833 distance: 37 - 45: 16.131 distance: 45 - 46: 25.334 distance: 46 - 47: 37.585 distance: 46 - 49: 36.377 distance: 47 - 48: 56.200 distance: 47 - 54: 40.862 distance: 47 - 60: 20.359 distance: 49 - 50: 6.789 distance: 50 - 51: 35.470 distance: 51 - 52: 31.841 distance: 51 - 53: 40.835 distance: 54 - 55: 22.877 distance: 55 - 56: 27.996 distance: 55 - 58: 19.012 distance: 56 - 57: 14.497 distance: 56 - 66: 46.671 distance: 58 - 59: 18.162 distance: 60 - 61: 38.204 distance: 61 - 62: 29.631 distance: 61 - 64: 39.566 distance: 62 - 63: 23.036 distance: 62 - 71: 21.935 distance: 64 - 65: 9.030 distance: 66 - 67: 34.561 distance: 67 - 68: 27.410 distance: 67 - 70: 23.009 distance: 68 - 76: 3.221 distance: 71 - 72: 21.886 distance: 72 - 73: 8.719 distance: 72 - 75: 25.609 distance: 73 - 74: 9.021 distance: 73 - 83: 16.815 distance: 76 - 77: 33.804 distance: 77 - 78: 40.849 distance: 77 - 80: 40.019 distance: 78 - 79: 13.328 distance: 78 - 90: 7.314 distance: 80 - 81: 56.614 distance: 80 - 82: 55.568 distance: 83 - 84: 8.574 distance: 84 - 85: 9.668 distance: 84 - 87: 17.798 distance: 85 - 86: 22.441 distance: 85 - 94: 21.248 distance: 87 - 88: 14.426 distance: 87 - 89: 10.060 distance: 90 - 91: 3.126 distance: 91 - 92: 10.761 distance: 92 - 93: 14.854 distance: 92 - 98: 16.232 distance: 94 - 95: 24.890 distance: 95 - 96: 13.867 distance: 96 - 97: 12.706 distance: 96 - 106: 16.288 distance: 98 - 99: 21.260 distance: 99 - 100: 22.604 distance: 99 - 102: 9.329 distance: 100 - 101: 11.085 distance: 100 - 114: 17.841 distance: 102 - 103: 48.139 distance: 103 - 104: 34.027 distance: 103 - 105: 40.043 distance: 106 - 107: 15.666 distance: 107 - 108: 7.581 distance: 107 - 110: 14.108 distance: 108 - 109: 6.460 distance: 108 - 119: 5.725 distance: 110 - 111: 36.754 distance: 111 - 112: 6.924 distance: 111 - 113: 17.778 distance: 114 - 115: 18.565 distance: 115 - 116: 13.684 distance: 115 - 118: 30.050 distance: 116 - 117: 10.325 distance: 116 - 124: 46.460 distance: 119 - 120: 6.918 distance: 120 - 121: 19.593 distance: 120 - 123: 16.400 distance: 121 - 122: 30.661 distance: 121 - 133: 11.263 distance: 124 - 125: 21.571 distance: 125 - 126: 16.645 distance: 125 - 128: 27.444 distance: 126 - 127: 10.880 distance: 126 - 142: 14.955 distance: 128 - 129: 24.048 distance: 129 - 130: 8.487 distance: 130 - 131: 7.233 distance: 130 - 132: 12.592 distance: 133 - 134: 10.778 distance: 134 - 135: 7.033 distance: 134 - 137: 20.915 distance: 135 - 136: 4.161 distance: 135 - 148: 12.176 distance: 137 - 138: 6.066 distance: 138 - 139: 18.342 distance: 139 - 140: 7.646 distance: 139 - 141: 10.424 distance: 142 - 143: 8.568 distance: 143 - 144: 18.888 distance: 143 - 146: 6.799 distance: 144 - 145: 14.232 distance: 144 - 154: 16.881 distance: 146 - 147: 7.925 distance: 148 - 149: 16.906 distance: 149 - 150: 34.271 distance: 149 - 152: 27.893 distance: 150 - 151: 6.857 distance: 150 - 154: 10.088 distance: 154 - 155: 3.558 distance: 155 - 156: 6.369 distance: 155 - 158: 28.357 distance: 156 - 157: 10.863 distance: 156 - 165: 15.490 distance: 158 - 159: 39.615 distance: 159 - 160: 14.605 distance: 160 - 161: 40.135 distance: 161 - 162: 52.261 distance: 162 - 163: 7.312