Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 3 23:33:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/05_2023/7cp9_30421_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/05_2023/7cp9_30421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/05_2023/7cp9_30421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/05_2023/7cp9_30421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/05_2023/7cp9_30421_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/05_2023/7cp9_30421_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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 11 5.49 5 S 36 5.16 5 C 5572 2.51 5 N 1390 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "I PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 348": "NH1" <-> "NH2" Residue "J PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 348": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 8530 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 312 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "E" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "F" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "G" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 646 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 646 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 272} Chain: "J" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 272} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.63, per 1000 atoms: 0.54 Number of scatterers: 8530 At special positions: 0 Unit cell: (122.694, 140.946, 100.386, 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 36 16.00 P 11 15.00 O 1521 8.00 N 1390 7.00 C 5572 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 2 sheets defined 36.3% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 Proline residue: A 42 - end of helix removed outlier: 4.419A pdb=" N LEU A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 39 removed outlier: 4.086A pdb=" N MET B 20 " --> pdb=" O MET B 16 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.630A pdb=" N ASP C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.631A pdb=" N ASP D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 Processing helix chain 'E' and resid 5 through 37 removed outlier: 5.665A pdb=" N ILE E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 49 through 52 Processing helix chain 'F' and resid 5 through 37 removed outlier: 5.664A pdb=" N ILE F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Proline residue: F 29 - end of helix Processing helix chain 'F' and resid 49 through 52 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 59 through 95 removed outlier: 3.876A pdb=" N ALA G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER G 81 " --> pdb=" O MET G 77 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 116 Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 59 through 95 removed outlier: 3.876A pdb=" N ALA H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 116 Processing helix chain 'I' and resid 84 through 91 removed outlier: 3.672A pdb=" N LYS I 91 " --> pdb=" O ARG I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 91 removed outlier: 3.673A pdb=" N LYS J 91 " --> pdb=" O ARG J 88 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 355 through 359 removed outlier: 5.607A pdb=" N GLY I 100 " --> pdb=" O PHE I 356 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU I 358 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS I 102 " --> pdb=" O LEU I 358 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN I 181 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU I 337 " --> pdb=" O LEU I 332 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 355 through 359 removed outlier: 5.607A pdb=" N GLY J 100 " --> pdb=" O PHE J 356 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU J 358 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS J 102 " --> pdb=" O LEU J 358 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN J 181 " --> pdb=" O PHE J 185 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE J 185 " --> pdb=" O GLN J 181 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE J 323 " --> pdb=" O ASP J 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU J 337 " --> pdb=" O LEU J 332 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1554 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: 2.43 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1316 1.30 - 1.43: 2165 1.43 - 1.56: 5121 1.56 - 1.68: 23 1.68 - 1.81: 62 Bond restraints: 8687 Sorted by residual: bond pdb=" C31 PC1 E 102 " pdb=" O31 PC1 E 102 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C21 PC1 E 102 " pdb=" O21 PC1 E 102 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C21 PC1 C 101 " pdb=" O21 PC1 C 101 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C31 PC1 F 102 " pdb=" O31 PC1 F 102 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C31 PC1 G 202 " pdb=" O31 PC1 G 202 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 8682 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.12: 249 107.12 - 113.87: 5162 113.87 - 120.62: 3381 120.62 - 127.37: 2750 127.37 - 134.12: 98 Bond angle restraints: 11640 Sorted by residual: angle pdb=" O12 PC1 C 101 " pdb=" P PC1 C 101 " pdb=" O14 PC1 C 101 " ideal model delta sigma weight residual 123.67 108.98 14.69 3.00e+00 1.11e-01 2.40e+01 angle pdb=" O12 PC1 E 102 " pdb=" P PC1 E 102 " pdb=" O14 PC1 E 102 " ideal model delta sigma weight residual 123.67 108.99 14.68 3.00e+00 1.11e-01 2.39e+01 angle pdb=" O12 PC1 G 201 " pdb=" P PC1 G 201 " pdb=" O14 PC1 G 201 " ideal model delta sigma weight residual 123.67 109.09 14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O12 PC1 G 202 " pdb=" P PC1 G 202 " pdb=" O14 PC1 G 202 " ideal model delta sigma weight residual 123.67 109.22 14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" O12 PC1 F 101 " pdb=" P PC1 F 101 " pdb=" O14 PC1 F 101 " ideal model delta sigma weight residual 123.67 109.23 14.44 3.00e+00 1.11e-01 2.32e+01 ... (remaining 11635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 4566 16.71 - 33.42: 424 33.42 - 50.13: 168 50.13 - 66.84: 62 66.84 - 83.55: 20 Dihedral angle restraints: 5240 sinusoidal: 2335 harmonic: 2905 Sorted by residual: dihedral pdb=" CA LYS A 47 " pdb=" C LYS A 47 " pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU A 45 " pdb=" C LEU A 45 " pdb=" N LYS A 46 " pdb=" CA LYS A 46 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP E 41 " pdb=" C ASP E 41 " pdb=" N PRO E 42 " pdb=" CA PRO E 42 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 849 0.038 - 0.075: 289 0.075 - 0.113: 87 0.113 - 0.151: 15 0.151 - 0.189: 1 Chirality restraints: 1241 Sorted by residual: chirality pdb=" CA THR A 41 " pdb=" N THR A 41 " pdb=" C THR A 41 " pdb=" CB THR A 41 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA ASP I 198 " pdb=" N ASP I 198 " pdb=" C ASP I 198 " pdb=" CB ASP I 198 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ASP J 198 " pdb=" N ASP J 198 " pdb=" C ASP J 198 " pdb=" CB ASP J 198 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1238 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 41 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO B 42 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 332 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO J 333 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO J 333 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 333 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 332 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO I 333 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 333 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 333 " -0.027 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 597 2.73 - 3.27: 7928 3.27 - 3.81: 12883 3.81 - 4.36: 15018 4.36 - 4.90: 27533 Nonbonded interactions: 63959 Sorted by model distance: nonbonded pdb=" OH TYR J 221 " pdb=" OE1 GLN J 223 " model vdw 2.183 2.440 nonbonded pdb=" OH TYR I 221 " pdb=" OE1 GLN I 223 " model vdw 2.183 2.440 nonbonded pdb=" OG SER I 122 " pdb=" O ILE I 124 " model vdw 2.263 2.440 nonbonded pdb=" OG SER J 122 " pdb=" O ILE J 124 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASN C 15 " pdb=" OG1 THR C 17 " model vdw 2.266 2.440 ... (remaining 63954 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 11 through 47) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 15 through 63) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 29 through 118 or resid 201 through 202)) selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 76 through 361) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 10.420 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 24.390 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.007 0.072 8687 Z= 0.473 Angle : 1.241 14.685 11640 Z= 0.522 Chirality : 0.042 0.189 1241 Planarity : 0.004 0.056 1431 Dihedral : 16.750 83.555 3370 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 7.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.25), residues: 997 helix: -0.82 (0.25), residues: 368 sheet: -1.22 (0.25), residues: 380 loop : -3.24 (0.35), residues: 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 258 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 21 residues processed: 301 average time/residue: 1.1228 time to fit residues: 359.9040 Evaluate side-chains 224 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 4 average time/residue: 0.6259 time to fit residues: 3.9585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN H 110 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 GLN I 220 HIS I 295 GLN J 163 GLN J 166 HIS J 181 GLN J 189 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8687 Z= 0.289 Angle : 0.722 8.638 11640 Z= 0.363 Chirality : 0.044 0.211 1241 Planarity : 0.005 0.047 1431 Dihedral : 14.971 89.515 1514 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 7.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.46 (0.27), residues: 997 helix: 0.34 (0.27), residues: 372 sheet: -1.08 (0.25), residues: 396 loop : -2.58 (0.39), residues: 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 208 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 33 residues processed: 250 average time/residue: 1.0774 time to fit residues: 288.2210 Evaluate side-chains 235 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 9 average time/residue: 0.3981 time to fit residues: 5.4320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 50.5073 > 50: distance: 57 - 168: 29.090 distance: 60 - 165: 16.635 distance: 69 - 156: 8.501 distance: 72 - 153: 9.085 distance: 80 - 143: 9.913 distance: 83 - 140: 6.991 distance: 92 - 128: 10.896 distance: 105 - 110: 27.177 distance: 110 - 111: 36.108 distance: 111 - 112: 16.129 distance: 111 - 114: 20.489 distance: 112 - 113: 23.898 distance: 112 - 118: 12.178 distance: 114 - 115: 34.715 distance: 115 - 117: 19.944 distance: 118 - 119: 18.562 distance: 118 - 124: 27.615 distance: 119 - 120: 10.448 distance: 119 - 122: 8.985 distance: 120 - 121: 13.894 distance: 120 - 125: 7.643 distance: 122 - 123: 15.746 distance: 123 - 124: 21.190 distance: 125 - 126: 23.514 distance: 126 - 127: 18.811 distance: 126 - 129: 18.947 distance: 127 - 128: 23.053 distance: 127 - 133: 16.483 distance: 129 - 130: 19.372 distance: 130 - 131: 9.729 distance: 130 - 132: 10.915 distance: 133 - 134: 28.006 distance: 133 - 240: 7.015 distance: 134 - 135: 21.352 distance: 134 - 137: 24.733 distance: 135 - 136: 15.217 distance: 135 - 140: 14.760 distance: 136 - 237: 11.483 distance: 137 - 138: 42.030 distance: 137 - 139: 28.919 distance: 140 - 141: 3.698 distance: 141 - 144: 20.312 distance: 142 - 143: 11.910 distance: 142 - 148: 16.617 distance: 144 - 145: 20.058 distance: 145 - 146: 16.867 distance: 145 - 147: 20.055 distance: 148 - 149: 13.203 distance: 148 - 228: 7.592 distance: 149 - 152: 10.753 distance: 150 - 151: 15.228 distance: 150 - 153: 10.445 distance: 151 - 225: 9.187 distance: 153 - 154: 13.249 distance: 154 - 155: 12.643 distance: 154 - 157: 5.128 distance: 155 - 156: 12.675 distance: 155 - 161: 32.154 distance: 157 - 158: 6.078 distance: 158 - 159: 6.273 distance: 158 - 160: 5.424 distance: 161 - 162: 34.620 distance: 161 - 216: 24.633 distance: 162 - 163: 29.974 distance: 163 - 164: 27.081 distance: 163 - 165: 38.583 distance: 164 - 213: 6.645 distance: 165 - 166: 7.009 distance: 166 - 167: 13.934 distance: 166 - 169: 32.810 distance: 167 - 168: 37.935 distance: 167 - 170: 41.723 distance: 170 - 171: 23.969 distance: 170 - 205: 24.930 distance: 171 - 172: 33.080 distance: 171 - 174: 34.676 distance: 172 - 173: 32.237 distance: 172 - 181: 21.200 distance: 173 - 202: 15.278 distance: 174 - 175: 21.909 distance: 175 - 176: 21.631 distance: 175 - 177: 8.326 distance: 176 - 178: 5.801 distance: 177 - 179: 12.199 distance: 178 - 180: 12.675 distance: 179 - 180: 17.268