Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 13:28:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/10_2023/8ott_17184_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/10_2023/8ott_17184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/10_2023/8ott_17184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/10_2023/8ott_17184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/10_2023/8ott_17184_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ott_17184/10_2023/8ott_17184_updated.pdb" } resolution = 3.3 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= 0.002 sd= 0.018 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 288 5.49 5 S 14 5.16 5 C 7231 2.51 5 N 2441 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 12973 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2969 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "M" Number of atoms: 538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 53, 269 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Conformer: "B" Number of residues, atoms: 53, 269 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "N" Number of atoms: 512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 51, 256 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 51, 256 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Residues with excluded nonbonded symmetry interactions: 104 residue: pdb=" N AASN M 353 " occ=0.50 ... (8 atoms not shown) pdb=" CB BASN M 353 " occ=0.50 residue: pdb=" N AVAL M 354 " occ=0.50 ... (8 atoms not shown) pdb=" CB BVAL M 354 " occ=0.50 residue: pdb=" N ALYS M 355 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS M 355 " occ=0.50 residue: pdb=" N AARG M 356 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG M 356 " occ=0.50 residue: pdb=" N AARG M 357 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG M 357 " occ=0.50 residue: pdb=" N ATHR M 358 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR M 358 " occ=0.50 residue: pdb=" N AHIS M 359 " occ=0.50 ... (8 atoms not shown) pdb=" CB BHIS M 359 " occ=0.50 residue: pdb=" N AASN M 360 " occ=0.50 ... (8 atoms not shown) pdb=" CB BASN M 360 " occ=0.50 residue: pdb=" N AVAL M 361 " occ=0.50 ... (8 atoms not shown) pdb=" CB BVAL M 361 " occ=0.50 residue: pdb=" N ALEU M 362 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU M 362 " occ=0.50 residue: pdb=" N AGLU M 363 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLU M 363 " occ=0.50 residue: pdb=" N AARG M 364 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG M 364 " occ=0.50 ... (remaining 92 not shown) Time building chain proxies: 7.33, per 1000 atoms: 0.57 Number of scatterers: 12973 At special positions: 0 Unit cell: (138.58, 114.92, 109.005, 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 14 16.00 P 288 15.00 O 2999 8.00 N 2441 7.00 C 7231 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 0 sheets defined 67.3% alpha, 0.0% beta 143 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 6.68 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.751A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.742A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.507A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.419A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.577A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.146A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.661A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 38 removed outlier: 4.708A pdb=" N GLY G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.773A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 380 Processing helix chain 'M' and resid 382 through 384 No H-bonds generated for 'chain 'M' and resid 382 through 384' Processing helix chain 'M' and resid 392 through 404 Processing helix chain 'N' and resid 24 through 49 Processing helix chain 'N' and resid 51 through 53 No H-bonds generated for 'chain 'N' and resid 51 through 53' Processing helix chain 'N' and resid 60 through 72 466 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2293 1.33 - 1.45: 4570 1.45 - 1.57: 6300 1.57 - 1.69: 574 1.69 - 1.81: 24 Bond restraints: 13761 Sorted by residual: bond pdb=" C3' DG J 101 " pdb=" C2' DG J 101 " ideal model delta sigma weight residual 1.525 1.560 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C3' DG I 99 " pdb=" C2' DG I 99 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C3' DG I 40 " pdb=" C2' DG I 40 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C1 PTD D 201 " pdb=" C2 PTD D 201 " ideal model delta sigma weight residual 1.499 1.531 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 PTD D 202 " pdb=" C2 PTD D 202 " ideal model delta sigma weight residual 1.499 1.531 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 13756 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.30: 1141 105.30 - 112.29: 7520 112.29 - 119.28: 4232 119.28 - 126.27: 6093 126.27 - 133.26: 865 Bond angle restraints: 19851 Sorted by residual: angle pdb=" C2' DG I 99 " pdb=" C1' DG I 99 " pdb=" N9 DG I 99 " ideal model delta sigma weight residual 113.50 118.08 -4.58 1.50e+00 4.44e-01 9.31e+00 angle pdb=" O4' DG I 67 " pdb=" C1' DG I 67 " pdb=" N9 DG I 67 " ideal model delta sigma weight residual 108.40 104.32 4.08 1.50e+00 4.44e-01 7.40e+00 angle pdb=" C ARG G 32 " pdb=" CA ARG G 32 " pdb=" CB ARG G 32 " ideal model delta sigma weight residual 110.81 106.48 4.33 1.60e+00 3.91e-01 7.32e+00 angle pdb=" CG ARG B 92 " pdb=" CD ARG B 92 " pdb=" NE ARG B 92 " ideal model delta sigma weight residual 112.00 106.19 5.81 2.20e+00 2.07e-01 6.98e+00 angle pdb=" C2' DC I 70 " pdb=" C1' DC I 70 " pdb=" N1 DC I 70 " ideal model delta sigma weight residual 113.50 117.42 -3.92 1.50e+00 4.44e-01 6.82e+00 ... (remaining 19846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 6026 31.68 - 63.37: 1242 63.37 - 95.05: 8 95.05 - 126.73: 0 126.73 - 158.41: 1 Dihedral angle restraints: 7277 sinusoidal: 4480 harmonic: 2797 Sorted by residual: dihedral pdb=" CA ALA G 14 " pdb=" C ALA G 14 " pdb=" N LYS G 15 " pdb=" CA LYS G 15 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " pdb=" P DC I 78 " ideal model delta sinusoidal sigma weight residual 220.00 61.59 158.41 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" CA TYR D 83 " pdb=" C TYR D 83 " pdb=" N ASN D 84 " pdb=" CA ASN D 84 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 7274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1728 0.045 - 0.089: 414 0.089 - 0.134: 108 0.134 - 0.179: 41 0.179 - 0.223: 4 Chirality restraints: 2295 Sorted by residual: chirality pdb=" CA LYS G 15 " pdb=" N LYS G 15 " pdb=" C LYS G 15 " pdb=" CB LYS G 15 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LYS F 77 " pdb=" N LYS F 77 " pdb=" C LYS F 77 " pdb=" CB LYS F 77 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C4' DG I 67 " pdb=" C5' DG I 67 " pdb=" O4' DG I 67 " pdb=" C3' DG I 67 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 2292 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 67 " 0.064 2.00e-02 2.50e+03 2.56e-02 1.96e+01 pdb=" N9 DG I 67 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DG I 67 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DG I 67 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DG I 67 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 67 " 0.013 2.00e-02 2.50e+03 pdb=" O6 DG I 67 " 0.021 2.00e-02 2.50e+03 pdb=" N1 DG I 67 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 67 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 67 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 67 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DG I 67 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 92 " 0.378 9.50e-02 1.11e+02 1.69e-01 1.77e+01 pdb=" NE ARG B 92 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 92 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 92 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 92 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 69 " 0.052 2.00e-02 2.50e+03 2.19e-02 1.31e+01 pdb=" N9 DA I 69 " -0.043 2.00e-02 2.50e+03 pdb=" C8 DA I 69 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 69 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 69 " 0.022 2.00e-02 2.50e+03 pdb=" N1 DA I 69 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 69 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DA I 69 " -0.009 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 5940 2.99 - 3.47: 12285 3.47 - 3.95: 25697 3.95 - 4.42: 28127 4.42 - 4.90: 37142 Nonbonded interactions: 109191 Sorted by model distance: nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.513 2.440 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.520 2.440 nonbonded pdb=" N6 DA I 69 " pdb=" O6 DG J 78 " model vdw 2.528 2.520 nonbonded pdb=" O LEU A 103 " pdb=" OG1 THR A 107 " model vdw 2.556 2.440 nonbonded pdb=" N GLN G 24 " pdb=" OE1 GLU G 56 " model vdw 2.559 2.520 ... (remaining 109186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 40 through 133 or resid 201 through 202)) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'G' and resid 10 through 116) } ncs_group { reference = (chain 'D' and (resid 32 through 124 or resid 201)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 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: 2.090 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: 7.300 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 43.220 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.005 0.035 13761 Z= 0.272 Angle : 0.774 5.811 19851 Z= 0.478 Chirality : 0.046 0.223 2295 Planarity : 0.010 0.169 1541 Dihedral : 24.445 158.413 5461 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.16 % Allowed : 0.79 % Favored : 99.05 % 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: 1.04 (0.24), residues: 939 helix: 0.97 (0.17), residues: 703 sheet: None (None), residues: 0 loop : 0.12 (0.37), residues: 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.4010 time to fit residues: 96.7722 Evaluate side-chains 116 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4182 time to fit residues: 1.6072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 49 HIS H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13761 Z= 0.226 Angle : 0.591 12.457 19851 Z= 0.347 Chirality : 0.036 0.200 2295 Planarity : 0.004 0.042 1541 Dihedral : 29.453 157.419 3963 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.27 % Allowed : 9.68 % Favored : 89.05 % 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: 3.34 (0.26), residues: 939 helix: 2.90 (0.19), residues: 699 sheet: None (None), residues: 0 loop : 0.07 (0.38), residues: 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.070 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 135 average time/residue: 0.3068 time to fit residues: 56.6506 Evaluate side-chains 116 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1219 time to fit residues: 2.2467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.0980 chunk 100 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13761 Z= 0.323 Angle : 0.599 7.028 19851 Z= 0.353 Chirality : 0.037 0.144 2295 Planarity : 0.004 0.034 1541 Dihedral : 30.018 162.459 3963 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.43 % Allowed : 11.75 % Favored : 86.83 % 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: 3.56 (0.27), residues: 939 helix: 3.14 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -0.14 (0.38), residues: 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 129 average time/residue: 0.2991 time to fit residues: 52.9117 Evaluate side-chains 107 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1153 time to fit residues: 1.7006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 50.0000 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13761 Z= 0.320 Angle : 0.580 7.846 19851 Z= 0.342 Chirality : 0.036 0.151 2295 Planarity : 0.004 0.031 1541 Dihedral : 29.992 159.684 3963 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.27 % Allowed : 11.75 % Favored : 86.98 % 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: 3.72 (0.27), residues: 939 helix: 3.27 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.030 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 113 average time/residue: 0.2740 time to fit residues: 43.6812 Evaluate side-chains 102 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1123 time to fit residues: 1.7427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13761 Z= 0.265 Angle : 0.558 6.234 19851 Z= 0.332 Chirality : 0.034 0.148 2295 Planarity : 0.004 0.032 1541 Dihedral : 29.810 159.469 3963 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.79 % Allowed : 13.02 % Favored : 86.19 % 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: 3.83 (0.27), residues: 939 helix: 3.39 (0.18), residues: 697 sheet: None (None), residues: 0 loop : -0.19 (0.38), residues: 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.963 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.2504 time to fit residues: 40.9340 Evaluate side-chains 104 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1593 time to fit residues: 1.7661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 50.0000 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13761 Z= 0.175 Angle : 0.545 10.609 19851 Z= 0.325 Chirality : 0.033 0.204 2295 Planarity : 0.004 0.033 1541 Dihedral : 29.361 157.463 3963 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.48 % Allowed : 14.44 % Favored : 85.08 % 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: 3.91 (0.27), residues: 939 helix: 3.48 (0.18), residues: 692 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 0.2488 time to fit residues: 45.6780 Evaluate side-chains 113 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.969 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.4406 time to fit residues: 1.6368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.0040 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 50.0000 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13761 Z= 0.236 Angle : 0.589 12.774 19851 Z= 0.342 Chirality : 0.034 0.303 2295 Planarity : 0.004 0.033 1541 Dihedral : 29.548 157.575 3963 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.95 % Allowed : 15.24 % Favored : 83.81 % 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: 3.84 (0.27), residues: 939 helix: 3.43 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.061 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.2414 time to fit residues: 40.2927 Evaluate side-chains 107 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1166 time to fit residues: 1.9402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 66.1097 > 50: distance: 12 - 41: 5.492 distance: 14 - 46: 3.468 distance: 18 - 51: 4.085 distance: 22 - 56: 4.944 distance: 26 - 61: 13.941 distance: 30 - 66: 8.445 distance: 33 - 41: 4.202 distance: 34 - 71: 8.995 distance: 39 - 76: 12.398 distance: 43 - 44: 7.023 distance: 43 - 51: 4.682 distance: 44 - 81: 4.684 distance: 47 - 48: 3.093 distance: 47 - 50: 3.357 distance: 49 - 86: 9.325 distance: 51 - 52: 8.426 distance: 52 - 53: 3.161 distance: 52 - 55: 4.723 distance: 53 - 54: 4.663 distance: 53 - 61: 3.429 distance: 54 - 91: 24.558 distance: 57 - 58: 4.972 distance: 57 - 60: 3.904 distance: 59 - 96: 3.459 distance: 61 - 62: 6.275 distance: 62 - 63: 4.570 distance: 62 - 65: 10.831 distance: 63 - 64: 9.538 distance: 63 - 71: 7.715 distance: 64 - 101: 38.013 distance: 66 - 67: 3.120 distance: 67 - 68: 6.287 distance: 67 - 70: 5.425 distance: 68 - 69: 4.869 distance: 68 - 76: 5.970 distance: 69 - 106: 6.620 distance: 71 - 72: 11.004 distance: 72 - 73: 6.542 distance: 72 - 75: 4.907 distance: 73 - 74: 3.378 distance: 74 - 111: 24.248 distance: 76 - 77: 4.474 distance: 77 - 78: 6.557 distance: 77 - 80: 14.240 distance: 78 - 86: 5.076 distance: 79 - 116: 10.685 distance: 81 - 82: 9.275 distance: 82 - 83: 7.787 distance: 82 - 85: 12.511 distance: 83 - 84: 7.347 distance: 83 - 91: 4.714 distance: 84 - 121: 16.567 distance: 86 - 87: 3.902 distance: 87 - 88: 3.907 distance: 88 - 89: 4.306 distance: 88 - 96: 7.426 distance: 89 - 126: 9.995 distance: 91 - 92: 6.295 distance: 92 - 93: 21.961 distance: 92 - 95: 10.351 distance: 93 - 94: 22.272 distance: 93 - 101: 26.283 distance: 94 - 131: 13.055 distance: 96 - 97: 7.323 distance: 97 - 98: 8.683 distance: 97 - 100: 7.533 distance: 98 - 99: 6.313 distance: 98 - 106: 10.211 distance: 99 - 136: 16.308 distance: 101 - 102: 43.587 distance: 102 - 103: 10.898 distance: 102 - 105: 23.212 distance: 103 - 104: 5.019 distance: 103 - 111: 4.125 distance: 104 - 141: 3.896 distance: 106 - 107: 3.917 distance: 107 - 108: 4.722 distance: 108 - 109: 3.909 distance: 108 - 116: 7.527 distance: 109 - 146: 23.179 distance: 112 - 115: 3.778 distance: 113 - 114: 4.823 distance: 113 - 121: 6.354 distance: 114 - 151: 7.871 distance: 116 - 117: 6.541 distance: 117 - 118: 5.772 distance: 117 - 120: 5.013 distance: 118 - 119: 3.949 distance: 118 - 126: 6.198 distance: 119 - 156: 11.362 distance: 122 - 123: 4.419 distance: 122 - 125: 3.272 distance: 123 - 124: 3.891 distance: 123 - 131: 3.086 distance: 124 - 161: 6.924 distance: 126 - 127: 4.294 distance: 127 - 128: 3.129 distance: 128 - 136: 3.243 distance: 129 - 166: 8.127 distance: 131 - 132: 6.612 distance: 132 - 133: 4.404 distance: 132 - 135: 7.854 distance: 133 - 134: 4.107 distance: 133 - 141: 4.714 distance: 134 - 171: 6.290 distance: 136 - 137: 3.639 distance: 137 - 138: 3.778 distance: 137 - 140: 8.062 distance: 138 - 146: 4.956 distance: 139 - 175: 3.460