Starting phenix.real_space_refine on Tue Dec 12 06:43:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/12_2023/5gaq_8015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/12_2023/5gaq_8015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/12_2023/5gaq_8015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/12_2023/5gaq_8015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/12_2023/5gaq_8015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/12_2023/5gaq_8015.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 13032 2.51 5 N 3465 2.21 5 O 4005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 294": "OE1" <-> "OE2" Residue "H TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 294": "OE1" <-> "OE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 294": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20574 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 10.55, per 1000 atoms: 0.51 Number of scatterers: 20574 At special positions: 0 Unit cell: (132.99, 134.42, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 4005 8.00 N 3465 7.00 C 13032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.46 Conformation dependent library (CDL) restraints added in 3.8 seconds 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4770 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 1.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 240 through 243 removed outlier: 3.513A pdb=" N GLN A 243 " --> pdb=" O ASN A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'B' and resid 240 through 243 removed outlier: 3.513A pdb=" N GLN B 243 " --> pdb=" O ASN B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'C' and resid 240 through 243 removed outlier: 3.508A pdb=" N GLN C 243 " --> pdb=" O ASN C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 240 through 243' Processing helix chain 'D' and resid 240 through 243 removed outlier: 3.507A pdb=" N GLN D 243 " --> pdb=" O ASN D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'E' and resid 240 through 243 removed outlier: 3.509A pdb=" N GLN E 243 " --> pdb=" O ASN E 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 240 through 243' Processing helix chain 'F' and resid 240 through 243 removed outlier: 3.515A pdb=" N GLN F 243 " --> pdb=" O ASN F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 240 through 243' Processing helix chain 'G' and resid 240 through 243 removed outlier: 3.511A pdb=" N GLN G 243 " --> pdb=" O ASN G 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 240 through 243' Processing helix chain 'H' and resid 240 through 243 removed outlier: 3.506A pdb=" N GLN H 243 " --> pdb=" O ASN H 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 240 through 243' Processing helix chain 'I' and resid 240 through 243 removed outlier: 3.508A pdb=" N GLN I 243 " --> pdb=" O ASN I 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 240 through 243' No hydrogen bonds 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: 0.06 Time building geometry restraints manager: 8.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6513 1.34 - 1.45: 2856 1.45 - 1.57: 11529 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 21024 Sorted by residual: bond pdb=" CA PRO A 108 " pdb=" C PRO A 108 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 6.09e+00 bond pdb=" CA PRO F 108 " pdb=" C PRO F 108 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 5.95e+00 bond pdb=" CA PRO D 108 " pdb=" C PRO D 108 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.79e+00 bond pdb=" CA PRO C 108 " pdb=" C PRO C 108 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.79e+00 bond pdb=" CA PRO G 108 " pdb=" C PRO G 108 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.70e+00 ... (remaining 21019 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.05: 530 107.05 - 113.79: 11654 113.79 - 120.54: 7943 120.54 - 127.28: 8139 127.28 - 134.03: 228 Bond angle restraints: 28494 Sorted by residual: angle pdb=" N ASN G 248 " pdb=" CA ASN G 248 " pdb=" C ASN G 248 " ideal model delta sigma weight residual 111.36 116.08 -4.72 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ASN C 248 " pdb=" CA ASN C 248 " pdb=" C ASN C 248 " ideal model delta sigma weight residual 111.36 116.07 -4.71 1.09e+00 8.42e-01 1.87e+01 angle pdb=" N ASN B 248 " pdb=" CA ASN B 248 " pdb=" C ASN B 248 " ideal model delta sigma weight residual 111.36 116.07 -4.71 1.09e+00 8.42e-01 1.87e+01 angle pdb=" N ASN E 248 " pdb=" CA ASN E 248 " pdb=" C ASN E 248 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.09e+00 8.42e-01 1.84e+01 angle pdb=" N ASN I 248 " pdb=" CA ASN I 248 " pdb=" C ASN I 248 " ideal model delta sigma weight residual 111.36 116.01 -4.65 1.09e+00 8.42e-01 1.82e+01 ... (remaining 28489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 11284 15.50 - 30.99: 911 30.99 - 46.49: 180 46.49 - 61.98: 36 61.98 - 77.48: 9 Dihedral angle restraints: 12420 sinusoidal: 4923 harmonic: 7497 Sorted by residual: dihedral pdb=" CA PHE E 70 " pdb=" C PHE E 70 " pdb=" N GLU E 71 " pdb=" CA GLU E 71 " ideal model delta harmonic sigma weight residual -180.00 -163.28 -16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PHE B 70 " pdb=" C PHE B 70 " pdb=" N GLU B 71 " pdb=" CA GLU B 71 " ideal model delta harmonic sigma weight residual 180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PHE I 70 " pdb=" C PHE I 70 " pdb=" N GLU I 71 " pdb=" CA GLU I 71 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 12417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1571 0.049 - 0.098: 1044 0.098 - 0.147: 255 0.147 - 0.197: 195 0.197 - 0.246: 103 Chirality restraints: 3168 Sorted by residual: chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE E 127 " pdb=" N ILE E 127 " pdb=" C ILE E 127 " pdb=" CB ILE E 127 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE I 127 " pdb=" N ILE I 127 " pdb=" C ILE I 127 " pdb=" CB ILE I 127 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3165 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 279 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C THR F 279 " 0.029 2.00e-02 2.50e+03 pdb=" O THR F 279 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN F 280 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 279 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C THR E 279 " 0.029 2.00e-02 2.50e+03 pdb=" O THR E 279 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN E 280 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 279 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C THR I 279 " -0.029 2.00e-02 2.50e+03 pdb=" O THR I 279 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN I 280 " 0.010 2.00e-02 2.50e+03 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4989 2.81 - 3.33: 18259 3.33 - 3.86: 36101 3.86 - 4.38: 40324 4.38 - 4.90: 72865 Nonbonded interactions: 172538 Sorted by model distance: nonbonded pdb=" OG SER E 82 " pdb=" OG1 THR F 57 " model vdw 2.289 2.440 nonbonded pdb=" OG SER F 82 " pdb=" OG1 THR G 57 " model vdw 2.289 2.440 nonbonded pdb=" OG SER D 82 " pdb=" OG1 THR E 57 " model vdw 2.289 2.440 nonbonded pdb=" OG1 THR A 57 " pdb=" OG SER I 82 " model vdw 2.290 2.440 nonbonded pdb=" OG SER G 82 " pdb=" OG1 THR H 57 " model vdw 2.290 2.440 ... (remaining 172533 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 3.420 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 46.390 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4972 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 : 0.006 0.044 21024 Z= 0.436 Angle : 1.016 6.166 28494 Z= 0.654 Chirality : 0.081 0.246 3168 Planarity : 0.003 0.028 3600 Dihedral : 11.967 77.477 7650 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.80 % Allowed : 5.84 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -3.69 (0.14), residues: 2574 helix: None (None), residues: 0 sheet: -2.39 (0.12), residues: 1386 loop : -2.35 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 20 HIS 0.006 0.002 HIS G 103 PHE 0.007 0.002 PHE D 266 TYR 0.016 0.002 TYR F 96 ARG 0.004 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 846 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 855 average time/residue: 0.4094 time to fit residues: 502.5778 Evaluate side-chains 467 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 463 time to evaluate : 2.358 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2158 time to fit residues: 4.7953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN B 48 ASN B 81 HIS ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS B 243 GLN B 263 ASN C 11 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 248 ASN C 263 ASN D 11 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN D 263 ASN E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 81 HIS ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 215 ASN E 243 GLN E 263 ASN F 11 GLN F 46 ASN F 81 HIS ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN F 147 GLN F 243 GLN G 11 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS G 103 HIS ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN G 263 ASN H 36 GLN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN H 263 ASN I 11 GLN I 36 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 263 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4949 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21024 Z= 0.260 Angle : 0.583 7.416 28494 Z= 0.313 Chirality : 0.048 0.172 3168 Planarity : 0.003 0.043 3600 Dihedral : 4.716 16.805 2844 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.85 % Allowed : 15.01 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -3.23 (0.14), residues: 2574 helix: None (None), residues: 0 sheet: -2.05 (0.13), residues: 1413 loop : -2.09 (0.15), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 206 HIS 0.007 0.002 HIS C 194 PHE 0.019 0.002 PHE A 209 TYR 0.013 0.002 TYR A 129 ARG 0.009 0.001 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 468 time to evaluate : 2.336 Fit side-chains outliers start: 87 outliers final: 44 residues processed: 534 average time/residue: 0.3065 time to fit residues: 254.1706 Evaluate side-chains 434 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 390 time to evaluate : 2.225 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1814 time to fit residues: 18.1948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 190 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 215 ASN A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 58 HIS C 81 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 248 ASN C 263 ASN D 11 GLN D 48 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN D 243 GLN D 263 ASN E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN E 248 ASN F 46 ASN F 58 HIS ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN G 11 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 HIS G 147 GLN ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN G 263 ASN H 48 ASN H 58 HIS ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN H 243 GLN H 263 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN I 81 HIS ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21024 Z= 0.194 Angle : 0.529 9.413 28494 Z= 0.283 Chirality : 0.047 0.154 3168 Planarity : 0.003 0.041 3600 Dihedral : 4.296 15.182 2844 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.66 % Allowed : 18.68 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -2.82 (0.14), residues: 2574 helix: None (None), residues: 0 sheet: -1.70 (0.13), residues: 1341 loop : -1.96 (0.14), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 206 HIS 0.006 0.001 HIS B 103 PHE 0.028 0.002 PHE A 209 TYR 0.013 0.001 TYR H 178 ARG 0.010 0.001 ARG H 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 450 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 20 residues processed: 489 average time/residue: 0.3134 time to fit residues: 237.7102 Evaluate side-chains 392 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 372 time to evaluate : 2.354 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2029 time to fit residues: 10.4923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 243 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 58 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 263 ASN D 11 GLN D 58 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN E 243 GLN F 11 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 HIS G 143 GLN G 147 GLN ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN G 263 ASN H 46 ASN H 48 ASN H 58 HIS ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 ASN H 243 GLN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4955 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21024 Z= 0.188 Angle : 0.506 8.244 28494 Z= 0.271 Chirality : 0.046 0.175 3168 Planarity : 0.003 0.034 3600 Dihedral : 4.119 15.609 2844 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.92 % Allowed : 19.21 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -2.49 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.42 (0.13), residues: 1341 loop : -1.82 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 206 HIS 0.005 0.001 HIS B 103 PHE 0.021 0.002 PHE C 209 TYR 0.014 0.001 TYR H 273 ARG 0.004 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 415 time to evaluate : 2.362 Fit side-chains outliers start: 66 outliers final: 34 residues processed: 457 average time/residue: 0.3146 time to fit residues: 223.9628 Evaluate side-chains 396 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 362 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1867 time to fit residues: 15.1860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 263 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 58 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 48 ASN D 58 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN F 243 GLN G 11 GLN ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN G 263 ASN H 48 ASN H 58 HIS ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN H 243 GLN H 263 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4955 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21024 Z= 0.245 Angle : 0.537 9.478 28494 Z= 0.288 Chirality : 0.047 0.199 3168 Planarity : 0.003 0.031 3600 Dihedral : 4.168 16.230 2844 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.30 % Allowed : 19.39 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -2.34 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.32 (0.13), residues: 1341 loop : -1.72 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 206 HIS 0.006 0.001 HIS B 103 PHE 0.014 0.002 PHE A 209 TYR 0.038 0.001 TYR H 273 ARG 0.003 0.000 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 386 time to evaluate : 1.816 Fit side-chains outliers start: 52 outliers final: 20 residues processed: 421 average time/residue: 0.2344 time to fit residues: 155.3625 Evaluate side-chains 387 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 367 time to evaluate : 2.455 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1871 time to fit residues: 10.1038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6803 > 50: distance: 93 - 98: 6.349 distance: 98 - 99: 8.840 distance: 99 - 100: 11.414 distance: 99 - 102: 14.586 distance: 100 - 101: 8.250 distance: 100 - 105: 10.917 distance: 102 - 103: 10.171 distance: 102 - 104: 29.289 distance: 105 - 106: 7.717 distance: 106 - 107: 16.509 distance: 106 - 109: 5.147 distance: 107 - 108: 10.067 distance: 107 - 113: 9.835 distance: 109 - 110: 7.066 distance: 109 - 111: 12.685 distance: 110 - 112: 27.731 distance: 113 - 114: 15.522 distance: 114 - 115: 8.056 distance: 114 - 117: 8.000 distance: 115 - 116: 11.924 distance: 115 - 120: 4.115 distance: 117 - 118: 14.179 distance: 117 - 119: 7.435 distance: 120 - 121: 4.883 distance: 121 - 122: 3.970 distance: 121 - 124: 12.398 distance: 122 - 123: 11.929 distance: 122 - 129: 15.328 distance: 124 - 125: 17.690 distance: 125 - 126: 4.870 distance: 126 - 127: 13.735 distance: 127 - 128: 6.365 distance: 129 - 130: 26.825 distance: 130 - 131: 6.094 distance: 131 - 132: 12.956 distance: 131 - 133: 13.087 distance: 133 - 134: 14.467 distance: 134 - 135: 5.408 distance: 134 - 137: 6.388 distance: 135 - 136: 27.660 distance: 135 - 141: 21.970 distance: 137 - 138: 19.994 distance: 138 - 139: 23.445 distance: 139 - 140: 9.988 distance: 141 - 142: 6.562 distance: 142 - 143: 9.791 distance: 142 - 145: 27.314 distance: 143 - 144: 15.461 distance: 145 - 146: 25.601 distance: 146 - 147: 40.338 distance: 147 - 148: 18.156 distance: 148 - 149: 31.170 distance: 151 - 152: 6.949 distance: 151 - 154: 15.463 distance: 152 - 153: 9.803 distance: 154 - 155: 29.925 distance: 155 - 156: 16.883 distance: 155 - 157: 14.709 distance: 158 - 159: 21.804 distance: 159 - 160: 25.749 distance: 159 - 162: 20.069 distance: 160 - 161: 25.185 distance: 162 - 163: 8.147 distance: 162 - 164: 38.787 distance: 166 - 167: 13.432 distance: 166 - 169: 11.228 distance: 167 - 168: 7.425 distance: 167 - 173: 29.129 distance: 169 - 170: 36.633 distance: 170 - 171: 4.705 distance: 170 - 172: 9.292