Starting phenix.real_space_refine on Sat Aug 3 19:24:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/08_2024/7cp9_30421.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/08_2024/7cp9_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_30421/08_2024/7cp9_30421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/08_2024/7cp9_30421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/08_2024/7cp9_30421.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cp9_30421/08_2024/7cp9_30421.cif" } resolution = 3.0 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= -0.001 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-dev-5409/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: 5.83, per 1000 atoms: 0.68 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: 3.62 Conformation dependent library (CDL) restraints added in 1.5 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... Secondary structure from input PDB file: 22 helices and 2 sheets defined 39.5% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 12 through 41 Processing helix chain 'A' and resid 41 through 46 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 40 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) removed outlier: 3.902A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.912A pdb=" N LEU B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'C' and resid 19 through 33 removed outlier: 3.630A pdb=" N ASP C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 60 Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.631A pdb=" N ASP D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 60 Processing helix chain 'E' and resid 5 through 38 removed outlier: 5.665A pdb=" N ILE E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Proline residue: E 29 - end of helix removed outlier: 4.156A pdb=" N ARG E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'F' and resid 5 through 38 removed outlier: 5.664A pdb=" N ILE F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 4.156A pdb=" N ARG F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'G' and resid 30 through 39 Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 58 through 96 removed outlier: 4.092A pdb=" N ALA G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) 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 96 through 117 Processing helix chain 'H' and resid 30 through 39 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 58 through 96 removed outlier: 4.091A pdb=" N ALA H 62 " --> pdb=" O ARG H 58 " (cutoff:3.500A) 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 96 through 117 Processing helix chain 'I' and resid 84 through 92 removed outlier: 3.603A pdb=" N ARG I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS I 90 " --> pdb=" O CYS I 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 92 " --> pdb=" O ARG I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 92 removed outlier: 3.602A pdb=" N ARG J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS J 90 " --> pdb=" O CYS J 86 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU J 92 " --> pdb=" O ARG J 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 100 through 107 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) 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) Processing sheet with id=AA2, first strand: chain 'J' and resid 100 through 107 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) 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) 568 hydrogen bonds defined for protein. 1620 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: 2.59 Time building geometry restraints manager: 3.73 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 - 17.61: 4649 17.61 - 35.21: 437 35.21 - 52.82: 182 52.82 - 70.42: 50 70.42 - 88.03: 21 Dihedral angle restraints: 5339 sinusoidal: 2434 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 5336 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: 595 2.73 - 3.27: 7923 3.27 - 3.81: 12858 3.81 - 4.36: 14991 4.36 - 4.90: 27520 Nonbonded interactions: 63887 Sorted by model distance: nonbonded pdb=" OH TYR J 221 " pdb=" OE1 GLN J 223 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR I 221 " pdb=" OE1 GLN I 223 " model vdw 2.183 3.040 nonbonded pdb=" OG SER I 122 " pdb=" O ILE I 124 " model vdw 2.263 3.040 nonbonded pdb=" OG SER J 122 " pdb=" O ILE J 124 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASN C 15 " pdb=" OG1 THR C 17 " model vdw 2.266 3.040 ... (remaining 63882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 4.000 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.960 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.900 ------------------------------------------------------------------------------- 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= 0.487 Angle : 1.241 14.685 11640 Z= 0.522 Chirality : 0.042 0.189 1241 Planarity : 0.004 0.056 1431 Dihedral : 17.402 88.028 3469 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 % Allowed : 10.04 % Favored : 82.92 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 57 HIS 0.003 0.001 HIS J 271 PHE 0.017 0.002 PHE A 43 TYR 0.009 0.001 TYR J 275 ARG 0.003 0.000 ARG B 39 *********************** 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 : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5327 (OUTLIER) cc_final: 0.4913 (tpp-160) REVERT: C 57 TRP cc_start: 0.5840 (OUTLIER) cc_final: 0.5115 (m100) REVERT: D 57 TRP cc_start: 0.3468 (OUTLIER) cc_final: 0.2925 (t-100) REVERT: F 34 LEU cc_start: 0.9042 (mt) cc_final: 0.8704 (mt) REVERT: G 76 LYS cc_start: 0.7863 (mptm) cc_final: 0.7212 (mmpt) REVERT: G 78 TYR cc_start: 0.8715 (t80) cc_final: 0.8387 (t80) REVERT: H 78 TYR cc_start: 0.8841 (t80) cc_final: 0.8619 (t80) REVERT: H 81 SER cc_start: 0.8942 (t) cc_final: 0.8729 (m) REVERT: H 109 GLU cc_start: 0.7017 (tt0) cc_final: 0.6808 (tt0) REVERT: I 265 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8251 (mm) REVERT: I 297 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8667 (m) REVERT: J 306 ASP cc_start: 0.7594 (p0) cc_final: 0.7253 (p0) outliers start: 59 outliers final: 21 residues processed: 301 average time/residue: 1.1127 time to fit residues: 356.4302 Evaluate side-chains 229 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 338 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.0070 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 GLN H 110 GLN I 163 GLN I 220 HIS I 295 GLN J 111 ASN J 163 GLN J 166 HIS J 181 GLN J 189 GLN J 223 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8687 Z= 0.204 Angle : 0.700 8.007 11640 Z= 0.348 Chirality : 0.043 0.200 1241 Planarity : 0.005 0.043 1431 Dihedral : 17.065 96.869 1656 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 6.93 % Allowed : 21.62 % Favored : 71.45 % 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: -1.27 (0.26), residues: 997 helix: 0.44 (0.27), residues: 378 sheet: -0.99 (0.25), residues: 396 loop : -2.44 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 188 HIS 0.005 0.001 HIS I 220 PHE 0.023 0.001 PHE G 67 TYR 0.017 0.001 TYR I 275 ARG 0.005 0.001 ARG D 60 *********************** 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 260 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 202 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7583 (mmm160) cc_final: 0.7357 (mmp80) REVERT: B 19 LYS cc_start: 0.6393 (mmmm) cc_final: 0.5959 (mmtp) REVERT: B 29 ARG cc_start: 0.7447 (tmt170) cc_final: 0.7137 (tmt170) REVERT: B 47 LYS cc_start: 0.7904 (tttp) cc_final: 0.5936 (ttpt) REVERT: C 38 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.4826 (tpp-160) REVERT: D 57 TRP cc_start: 0.3842 (OUTLIER) cc_final: 0.2932 (t-100) REVERT: F 34 LEU cc_start: 0.9018 (mt) cc_final: 0.8674 (mt) REVERT: G 76 LYS cc_start: 0.7857 (mptm) cc_final: 0.7250 (mmtt) REVERT: G 77 MET cc_start: 0.7633 (ptt) cc_final: 0.7355 (ptp) REVERT: G 78 TYR cc_start: 0.8731 (t80) cc_final: 0.8452 (t80) REVERT: H 77 MET cc_start: 0.5919 (ptt) cc_final: 0.5256 (tmt) REVERT: H 78 TYR cc_start: 0.8857 (t80) cc_final: 0.8607 (t80) REVERT: H 81 SER cc_start: 0.8872 (t) cc_final: 0.8578 (m) REVERT: J 176 MET cc_start: 0.6435 (mpt) cc_final: 0.6154 (mpt) outliers start: 58 outliers final: 28 residues processed: 240 average time/residue: 1.0427 time to fit residues: 267.2508 Evaluate side-chains 223 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 338 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN G 75 GLN I 140 GLN I 220 HIS ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 ASN J 163 GLN J 181 GLN J 189 GLN J 223 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8687 Z= 0.233 Angle : 0.674 8.620 11640 Z= 0.341 Chirality : 0.043 0.188 1241 Planarity : 0.004 0.044 1431 Dihedral : 16.505 89.151 1642 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 8.12 % Allowed : 23.30 % Favored : 68.58 % 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: -0.81 (0.27), residues: 997 helix: 0.83 (0.27), residues: 378 sheet: -0.77 (0.25), residues: 396 loop : -2.14 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 188 HIS 0.004 0.001 HIS J 112 PHE 0.023 0.002 PHE B 31 TYR 0.020 0.002 TYR B 34 ARG 0.006 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 3 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 272 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 204 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.7935 (tttp) cc_final: 0.5960 (ttpt) REVERT: C 38 ARG cc_start: 0.5265 (OUTLIER) cc_final: 0.4872 (tpp-160) REVERT: C 49 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7750 (mp) REVERT: D 49 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7123 (tt) REVERT: D 57 TRP cc_start: 0.3958 (OUTLIER) cc_final: 0.2891 (t-100) REVERT: F 34 LEU cc_start: 0.9039 (mt) cc_final: 0.8695 (mt) REVERT: G 76 LYS cc_start: 0.7814 (mptm) cc_final: 0.7228 (mmtt) REVERT: G 77 MET cc_start: 0.7622 (ptt) cc_final: 0.7379 (ptp) REVERT: G 78 TYR cc_start: 0.8793 (t80) cc_final: 0.8527 (t80) REVERT: H 81 SER cc_start: 0.8859 (t) cc_final: 0.8561 (m) REVERT: H 117 ARG cc_start: 0.3330 (OUTLIER) cc_final: 0.1417 (mmm-85) REVERT: I 315 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8336 (mtmm) REVERT: J 114 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: J 176 MET cc_start: 0.6373 (mpt) cc_final: 0.6100 (mpt) REVERT: J 180 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8712 (t) REVERT: J 337 LEU cc_start: 0.8622 (tp) cc_final: 0.8415 (mt) outliers start: 68 outliers final: 38 residues processed: 246 average time/residue: 1.0379 time to fit residues: 272.6257 Evaluate side-chains 247 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 0.0770 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 10 GLN F 20 GLN I 220 HIS I 295 GLN J 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8687 Z= 0.272 Angle : 0.697 8.922 11640 Z= 0.351 Chirality : 0.043 0.188 1241 Planarity : 0.005 0.045 1431 Dihedral : 16.326 88.868 1642 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 8.36 % Allowed : 24.73 % Favored : 66.91 % 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: -0.60 (0.27), residues: 997 helix: 0.96 (0.27), residues: 376 sheet: -0.58 (0.26), residues: 396 loop : -2.11 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 57 HIS 0.007 0.001 HIS J 112 PHE 0.029 0.002 PHE G 67 TYR 0.019 0.002 TYR J 275 ARG 0.004 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 4 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 280 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 210 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 LYS cc_start: 0.6604 (mmmm) cc_final: 0.6177 (mmtp) REVERT: B 47 LYS cc_start: 0.7925 (tttp) cc_final: 0.5897 (ttpt) REVERT: C 38 ARG cc_start: 0.5323 (OUTLIER) cc_final: 0.4855 (tpp-160) REVERT: C 43 ARG cc_start: 0.8084 (tmt-80) cc_final: 0.7835 (ptm-80) REVERT: D 57 TRP cc_start: 0.4137 (OUTLIER) cc_final: 0.2789 (t-100) REVERT: F 34 LEU cc_start: 0.9070 (mt) cc_final: 0.8719 (mt) REVERT: G 76 LYS cc_start: 0.7807 (mptm) cc_final: 0.7217 (mmtt) REVERT: G 77 MET cc_start: 0.7579 (ptt) cc_final: 0.7298 (ptp) REVERT: G 78 TYR cc_start: 0.8838 (t80) cc_final: 0.8596 (t80) REVERT: G 87 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8510 (mp) REVERT: G 110 GLN cc_start: 0.6867 (tm-30) cc_final: 0.6587 (tt0) REVERT: H 79 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7124 (tmt170) REVERT: H 81 SER cc_start: 0.8885 (t) cc_final: 0.8564 (m) REVERT: H 117 ARG cc_start: 0.3384 (OUTLIER) cc_final: 0.1583 (mmm-85) REVERT: I 315 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: J 84 GLU cc_start: 0.7049 (pp20) cc_final: 0.6301 (pp20) REVERT: J 114 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: J 176 MET cc_start: 0.6342 (mpt) cc_final: 0.6110 (mpt) REVERT: J 180 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8699 (t) outliers start: 70 outliers final: 41 residues processed: 250 average time/residue: 1.0554 time to fit residues: 282.1060 Evaluate side-chains 253 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 317 SER Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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: 63.2784 > 50: distance: 11 - 18: 13.222 distance: 18 - 19: 17.792 distance: 19 - 20: 25.627 distance: 19 - 22: 31.304 distance: 20 - 21: 16.651 distance: 20 - 27: 3.786 distance: 21 - 54: 26.337 distance: 22 - 23: 10.318 distance: 23 - 24: 30.063 distance: 24 - 25: 14.796 distance: 24 - 26: 25.472 distance: 27 - 28: 19.607 distance: 28 - 29: 41.859 distance: 28 - 31: 24.480 distance: 29 - 30: 5.562 distance: 29 - 33: 24.840 distance: 31 - 32: 21.050 distance: 33 - 34: 11.092 distance: 34 - 35: 28.596 distance: 34 - 37: 5.635 distance: 35 - 36: 35.538 distance: 35 - 43: 20.294 distance: 36 - 69: 21.834 distance: 37 - 38: 9.865 distance: 38 - 39: 19.648 distance: 38 - 40: 13.218 distance: 39 - 41: 22.913 distance: 40 - 42: 16.983 distance: 41 - 42: 20.958 distance: 43 - 44: 20.361 distance: 44 - 45: 26.360 distance: 44 - 47: 5.377 distance: 45 - 46: 42.072 distance: 45 - 54: 13.433 distance: 47 - 48: 6.349 distance: 48 - 49: 23.928 distance: 49 - 50: 20.333 distance: 50 - 51: 7.614 distance: 51 - 52: 10.150 distance: 51 - 53: 5.580 distance: 54 - 55: 9.691 distance: 55 - 56: 11.910 distance: 55 - 58: 21.500 distance: 56 - 57: 22.745 distance: 56 - 63: 14.491 distance: 58 - 59: 10.355 distance: 59 - 60: 18.367 distance: 60 - 61: 22.960 distance: 61 - 62: 9.505 distance: 63 - 64: 18.513 distance: 64 - 65: 15.950 distance: 64 - 67: 16.854 distance: 65 - 66: 18.066 distance: 65 - 69: 20.997 distance: 67 - 68: 37.837 distance: 69 - 70: 6.892 distance: 70 - 71: 5.665 distance: 70 - 73: 9.366 distance: 71 - 72: 11.414 distance: 71 - 78: 15.667 distance: 73 - 74: 6.173 distance: 74 - 75: 9.631 distance: 75 - 76: 19.653 distance: 76 - 77: 11.863 distance: 78 - 79: 37.010 distance: 79 - 80: 10.366 distance: 79 - 82: 10.990 distance: 80 - 81: 6.937 distance: 80 - 87: 12.880 distance: 82 - 83: 18.627 distance: 83 - 84: 13.064 distance: 84 - 85: 7.315 distance: 84 - 86: 4.423 distance: 87 - 88: 12.697 distance: 88 - 89: 23.679 distance: 88 - 91: 37.853 distance: 89 - 90: 9.373 distance: 89 - 95: 35.635 distance: 91 - 92: 27.916 distance: 92 - 93: 18.486 distance: 92 - 94: 25.027 distance: 95 - 96: 35.464 distance: 96 - 97: 57.997 distance: 96 - 99: 48.795 distance: 97 - 98: 8.286 distance: 97 - 106: 29.064 distance: 99 - 100: 15.445 distance: 100 - 101: 18.180 distance: 100 - 102: 22.886 distance: 101 - 103: 26.920 distance: 102 - 104: 32.590 distance: 103 - 105: 27.342 distance: 104 - 105: 15.270