Starting phenix.real_space_refine (version: dev) on Thu Feb 23 16:04:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/02_2023/5gaq_8015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/02_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_8015/02_2023/5gaq_8015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/02_2023/5gaq_8015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/02_2023/5gaq_8015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/02_2023/5gaq_8015.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 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-dev-4877/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: 11.36, per 1000 atoms: 0.55 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: 7.59 Conformation dependent library (CDL) restraints added in 2.9 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: 0.13 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: 0.07 Time building geometry restraints manager: 8.26 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 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. 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: 0.460 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: 4.170 Check model and map are aligned: 0.260 Process input model: 42.910 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5009 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 : 1.015 6.166 28494 Z= 0.653 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 % 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 *********************** 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 : 2.644 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: 0.3858 time to fit residues: 469.5425 Evaluate side-chains 467 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 463 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2044 time to fit residues: 5.0160 ------------------------------------------------------------------------------- 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 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 263 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4996 moved from start: 0.3189 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= 0.257 Angle : 0.585 7.178 28494 Z= 0.313 Chirality : 0.048 0.166 3168 Planarity : 0.003 0.043 3600 Dihedral : 4.717 16.784 2844 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 3.76 % 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: -3.27 (0.14), residues: 2574 helix: None (None), residues: 0 sheet: -2.09 (0.13), residues: 1395 loop : -2.10 (0.14), residues: 1179 *********************** 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 554 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 469 time to evaluate : 2.497 Fit side-chains outliers start: 85 outliers final: 43 residues processed: 534 average time/residue: 0.3111 time to fit residues: 258.3442 Evaluate side-chains 435 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 392 time to evaluate : 2.559 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.1867 time to fit residues: 18.3906 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 155 optimal weight: 0.0000 chunk 63 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 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 ** 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 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 48 ASN 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 215 ASN H 243 GLN H 263 ASN ** 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: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4996 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 21024 Z= 0.191 Angle : 0.533 10.128 28494 Z= 0.284 Chirality : 0.047 0.146 3168 Planarity : 0.003 0.039 3600 Dihedral : 4.331 15.588 2844 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 2.57 % 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: -2.84 (0.14), residues: 2574 helix: None (None), residues: 0 sheet: -1.70 (0.13), residues: 1341 loop : -1.98 (0.14), residues: 1233 *********************** 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 490 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 432 time to evaluate : 2.574 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 22 residues processed: 471 average time/residue: 0.3167 time to fit residues: 230.8966 Evaluate side-chains 404 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 382 time to evaluate : 2.618 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2087 time to fit residues: 11.7260 ------------------------------------------------------------------------------- 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: 2.9990 chunk 172 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 243 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 0.0000 chunk 65 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 ** 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 81 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 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN 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 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 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 46 ASN H 58 HIS H 81 HIS 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: 0.5007 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 21024 Z= 0.144 Angle : 0.488 9.226 28494 Z= 0.261 Chirality : 0.046 0.166 3168 Planarity : 0.003 0.037 3600 Dihedral : 4.022 15.363 2844 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 2.04 % 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: -1.40 (0.13), residues: 1341 loop : -1.84 (0.14), residues: 1233 *********************** 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 474 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 428 time to evaluate : 2.654 Fit side-chains outliers start: 46 outliers final: 23 residues processed: 461 average time/residue: 0.3052 time to fit residues: 221.0811 Evaluate side-chains 394 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 371 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1860 time to fit residues: 11.2913 ------------------------------------------------------------------------------- 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: 8.9990 chunk 138 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** 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 58 HIS ** 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 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 48 ASN ** 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 58 HIS ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN F 243 GLN G 11 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 ASN G 243 GLN G 263 ASN H 48 ASN H 58 HIS 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 119 ASN I 243 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5006 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 21024 Z= 0.170 Angle : 0.496 10.534 28494 Z= 0.266 Chirality : 0.046 0.139 3168 Planarity : 0.003 0.032 3600 Dihedral : 3.935 16.087 2844 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 2.48 % 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: -2.27 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.21 (0.13), residues: 1341 loop : -1.75 (0.15), residues: 1233 *********************** 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 456 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 400 time to evaluate : 2.340 Fit side-chains outliers start: 56 outliers final: 24 residues processed: 440 average time/residue: 0.3113 time to fit residues: 215.1354 Evaluate side-chains 379 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 355 time to evaluate : 2.491 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1952 time to fit residues: 12.2690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** 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 48 ASN B 58 HIS ** 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 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN D 243 GLN ** 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 58 HIS ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN F 243 GLN G 11 GLN G 143 GLN G 263 ASN H 48 ASN H 58 HIS H 243 GLN H 263 ASN I 11 GLN ** 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: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 21024 Z= 0.261 Angle : 0.544 7.798 28494 Z= 0.292 Chirality : 0.047 0.179 3168 Planarity : 0.003 0.033 3600 Dihedral : 4.129 14.909 2844 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.81 % 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: -2.16 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.18 (0.13), residues: 1341 loop : -1.63 (0.15), residues: 1233 *********************** REFINEMENT MACRO_CYCLE 6 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 416 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 375 time to evaluate : 2.615 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 16 residues processed: 396 average time/residue: 0.3109 time to fit residues: 193.7381 Evaluate side-chains 372 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 356 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1927 time to fit residues: 9.1875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 242 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 215 ASN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 58 HIS ** 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 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 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 ASN G 263 ASN H 48 ASN H 58 HIS 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5008 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 21024 Z= 0.125 Angle : 0.490 10.971 28494 Z= 0.261 Chirality : 0.046 0.139 3168 Planarity : 0.003 0.034 3600 Dihedral : 3.826 14.307 2844 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.06 % 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: -1.97 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -0.92 (0.14), residues: 1323 loop : -1.67 (0.15), residues: 1251 *********************** REFINEMENT MACRO_CYCLE 7 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 419 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 395 time to evaluate : 2.553 Fit side-chains outliers start: 24 outliers final: 6 residues processed: 407 average time/residue: 0.3058 time to fit residues: 195.1844 Evaluate side-chains 359 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 353 time to evaluate : 2.396 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1867 time to fit residues: 5.3610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** 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 48 ASN B 58 HIS ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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** G 11 GLN G 215 ASN G 263 ASN H 58 HIS H 119 ASN H 243 GLN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5005 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 21024 Z= 0.239 Angle : 0.543 9.692 28494 Z= 0.292 Chirality : 0.047 0.187 3168 Planarity : 0.003 0.036 3600 Dihedral : 4.017 14.670 2844 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 1.68 % 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: -1.97 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.05 (0.13), residues: 1359 loop : -1.50 (0.16), residues: 1215 *********************** REFINEMENT MACRO_CYCLE 8 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 402 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 364 time to evaluate : 2.504 Fit side-chains outliers start: 38 outliers final: 20 residues processed: 381 average time/residue: 0.3031 time to fit residues: 182.8309 Evaluate side-chains 378 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 358 time to evaluate : 2.615 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1853 time to fit residues: 10.3836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** 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 58 HIS ** 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 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 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN G 11 GLN G 215 ASN G 263 ASN H 58 HIS H 243 GLN H 263 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5012 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 21024 Z= 0.150 Angle : 0.515 8.706 28494 Z= 0.275 Chirality : 0.047 0.335 3168 Planarity : 0.003 0.034 3600 Dihedral : 3.857 14.862 2844 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.62 % 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: -1.80 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -0.86 (0.14), residues: 1341 loop : -1.49 (0.16), residues: 1233 *********************** REFINEMENT MACRO_CYCLE 9 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 379 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 365 time to evaluate : 2.700 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 374 average time/residue: 0.3200 time to fit residues: 190.7223 Evaluate side-chains 355 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 348 time to evaluate : 2.642 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2027 time to fit residues: 6.2484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.8980 chunk 146 optimal weight: 0.0870 chunk 113 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 251 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 58 HIS B 117 GLN B 243 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN G 11 GLN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 ASN G 263 ASN H 58 HIS H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5022 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 21024 Z= 0.124 Angle : 0.505 8.688 28494 Z= 0.270 Chirality : 0.047 0.352 3168 Planarity : 0.003 0.036 3600 Dihedral : 3.713 14.994 2844 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.40 % 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: -1.67 (0.16), residues: 2574 helix: None (None), residues: 0 sheet: -0.72 (0.14), residues: 1341 loop : -1.48 (0.16), residues: 1233 ********************** REFINEMENT MACRO_CYCLE 10 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 383 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 374 time to evaluate : 2.429 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 376 average time/residue: 0.3104 time to fit residues: 182.4805 Evaluate side-chains 349 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 345 time to evaluate : 2.398 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2025 time to fit residues: 4.7918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 205 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 58 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 46 ASN D 48 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN G 11 GLN G 215 ASN G 263 ASN H 58 HIS H 263 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095851 restraints weight = 28196.254| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.32 r_work: 0.3193 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 21024 Z= 0.258 Angle : 0.573 8.336 28494 Z= 0.306 Chirality : 0.048 0.362 3168 Planarity : 0.003 0.039 3600 Dihedral : 4.016 19.048 2844 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.66 % 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: -1.76 (0.16), residues: 2574 helix: None (None), residues: 0 sheet: -0.86 (0.14), residues: 1359 loop : -1.43 (0.16), residues: 1215 =============================================================================== Job complete usr+sys time: 4870.28 seconds wall clock time: 89 minutes 15.24 seconds (5355.24 seconds total)