Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 19:16:46 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/12_2021/7b03_11955_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/12_2021/7b03_11955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/12_2021/7b03_11955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/12_2021/7b03_11955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/12_2021/7b03_11955_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/12_2021/7b03_11955_updated.pdb" } resolution = 2.93 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= 0.000 sd= 0.442 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "B" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "D" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "E" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.14, per 1000 atoms: 0.59 Number of scatterers: 8670 At special positions: 0 Unit cell: (103.2, 100.62, 67.08, 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 55 16.00 O 1470 8.00 N 1290 7.00 C 5855 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 Amimo 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.784A pdb=" N ARG A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 86 removed outlier: 4.342A pdb=" N THR A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 115 Proline residue: A 104 - end of helix removed outlier: 4.214A pdb=" N PHE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 143 Processing helix chain 'A' and resid 149 through 168 Processing helix chain 'A' and resid 171 through 178 removed outlier: 4.111A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 198 through 208 Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 220 through 232 Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'B' and resid 31 through 54 removed outlier: 3.783A pdb=" N ARG B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 86 removed outlier: 4.342A pdb=" N THR B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 79 " --> pdb=" O TRP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 115 Proline residue: B 104 - end of helix removed outlier: 4.214A pdb=" N PHE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 149 through 168 Processing helix chain 'B' and resid 171 through 178 removed outlier: 4.111A pdb=" N THR B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 198 through 208 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 220 through 232 Processing helix chain 'B' and resid 234 through 248 Processing helix chain 'C' and resid 31 through 54 removed outlier: 3.783A pdb=" N ARG C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 86 removed outlier: 4.342A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 79 " --> pdb=" O TRP C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 115 Proline residue: C 104 - end of helix removed outlier: 4.214A pdb=" N PHE C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 143 Processing helix chain 'C' and resid 149 through 168 Processing helix chain 'C' and resid 171 through 178 removed outlier: 4.112A pdb=" N THR C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 Processing helix chain 'C' and resid 198 through 208 Proline residue: C 202 - end of helix Processing helix chain 'C' and resid 220 through 232 Processing helix chain 'C' and resid 234 through 248 Processing helix chain 'D' and resid 31 through 54 removed outlier: 3.784A pdb=" N ARG D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 86 removed outlier: 4.343A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 79 " --> pdb=" O TRP D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 115 Proline residue: D 104 - end of helix removed outlier: 4.214A pdb=" N PHE D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 143 Processing helix chain 'D' and resid 149 through 168 Processing helix chain 'D' and resid 171 through 178 removed outlier: 4.112A pdb=" N THR D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 196 Processing helix chain 'D' and resid 198 through 208 Proline residue: D 202 - end of helix Processing helix chain 'D' and resid 220 through 232 Processing helix chain 'D' and resid 234 through 248 Processing helix chain 'E' and resid 31 through 54 removed outlier: 3.783A pdb=" N ARG E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 86 removed outlier: 4.342A pdb=" N THR E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR E 79 " --> pdb=" O TRP E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 115 Proline residue: E 104 - end of helix removed outlier: 4.214A pdb=" N PHE E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 143 Processing helix chain 'E' and resid 149 through 168 Processing helix chain 'E' and resid 171 through 178 removed outlier: 4.112A pdb=" N THR E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 196 Processing helix chain 'E' and resid 198 through 208 Proline residue: E 202 - end of helix Processing helix chain 'E' and resid 220 through 232 Processing helix chain 'E' and resid 234 through 248 640 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1288 1.32 - 1.44: 2758 1.44 - 1.57: 4789 1.57 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 8930 Sorted by residual: bond pdb=" C6 RET D 301 " pdb=" C7 RET D 301 " ideal model delta sigma weight residual 1.448 1.503 -0.055 1.10e-02 8.26e+03 2.46e+01 bond pdb=" C6 RET C 301 " pdb=" C7 RET C 301 " ideal model delta sigma weight residual 1.448 1.503 -0.055 1.10e-02 8.26e+03 2.46e+01 bond pdb=" C6 RET A 301 " pdb=" C7 RET A 301 " ideal model delta sigma weight residual 1.448 1.502 -0.054 1.10e-02 8.26e+03 2.45e+01 bond pdb=" C6 RET E 301 " pdb=" C7 RET E 301 " ideal model delta sigma weight residual 1.448 1.502 -0.054 1.10e-02 8.26e+03 2.44e+01 bond pdb=" C6 RET B 301 " pdb=" C7 RET B 301 " ideal model delta sigma weight residual 1.448 1.502 -0.054 1.10e-02 8.26e+03 2.43e+01 ... (remaining 8925 not shown) Histogram of bond angle deviations from ideal: 91.46 - 99.96: 15 99.96 - 108.46: 338 108.46 - 116.97: 5525 116.97 - 125.47: 6077 125.47 - 133.97: 240 Bond angle restraints: 12195 Sorted by residual: angle pdb=" C17 RET B 301 " pdb=" C1 RET B 301 " pdb=" C6 RET B 301 " ideal model delta sigma weight residual 110.14 98.20 11.94 1.42e+00 4.99e-01 7.12e+01 angle pdb=" C17 RET E 301 " pdb=" C1 RET E 301 " pdb=" C6 RET E 301 " ideal model delta sigma weight residual 110.14 98.21 11.93 1.42e+00 4.99e-01 7.11e+01 angle pdb=" C17 RET D 301 " pdb=" C1 RET D 301 " pdb=" C6 RET D 301 " ideal model delta sigma weight residual 110.14 98.22 11.92 1.42e+00 4.99e-01 7.10e+01 angle pdb=" C17 RET C 301 " pdb=" C1 RET C 301 " pdb=" C6 RET C 301 " ideal model delta sigma weight residual 110.14 98.22 11.92 1.42e+00 4.99e-01 7.09e+01 angle pdb=" C17 RET A 301 " pdb=" C1 RET A 301 " pdb=" C6 RET A 301 " ideal model delta sigma weight residual 110.14 98.22 11.92 1.42e+00 4.99e-01 7.09e+01 ... (remaining 12190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 4795 23.96 - 47.93: 95 47.93 - 71.89: 15 71.89 - 95.85: 15 95.85 - 119.81: 10 Dihedral angle restraints: 4930 sinusoidal: 1785 harmonic: 3145 Sorted by residual: dihedral pdb=" C2 RET E 301 " pdb=" C3 RET E 301 " pdb=" C4 RET E 301 " pdb=" C5 RET E 301 " ideal model delta sinusoidal sigma weight residual 52.08 -67.73 119.81 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C2 RET A 301 " pdb=" C3 RET A 301 " pdb=" C4 RET A 301 " pdb=" C5 RET A 301 " ideal model delta sinusoidal sigma weight residual 52.08 -67.71 119.79 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C2 RET D 301 " pdb=" C3 RET D 301 " pdb=" C4 RET D 301 " pdb=" C5 RET D 301 " ideal model delta sinusoidal sigma weight residual 52.08 -67.70 119.78 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 699 0.026 - 0.051: 402 0.051 - 0.077: 200 0.077 - 0.102: 50 0.102 - 0.128: 19 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CA TYR E 201 " pdb=" N TYR E 201 " pdb=" C TYR E 201 " pdb=" CB TYR E 201 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA TYR D 201 " pdb=" N TYR D 201 " pdb=" C TYR D 201 " pdb=" CB TYR D 201 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA TYR A 201 " pdb=" N TYR A 201 " pdb=" C TYR A 201 " pdb=" CB TYR A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1367 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 229 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C PHE E 229 " 0.020 2.00e-02 2.50e+03 pdb=" O PHE E 229 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL E 230 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 229 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C PHE B 229 " -0.020 2.00e-02 2.50e+03 pdb=" O PHE B 229 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL B 230 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 229 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C PHE A 229 " -0.020 2.00e-02 2.50e+03 pdb=" O PHE A 229 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 230 " 0.007 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 548 2.73 - 3.27: 9387 3.27 - 3.82: 15420 3.82 - 4.36: 18140 4.36 - 4.90: 31031 Nonbonded interactions: 74526 Sorted by model distance: nonbonded pdb=" OH TYR E 77 " pdb=" OD2 ASP E 228 " model vdw 2.190 2.440 nonbonded pdb=" OH TYR C 77 " pdb=" OD2 ASP C 228 " model vdw 2.190 2.440 nonbonded pdb=" OH TYR B 77 " pdb=" OD2 ASP B 228 " model vdw 2.190 2.440 nonbonded pdb=" OH TYR A 77 " pdb=" OD2 ASP A 228 " model vdw 2.191 2.440 nonbonded pdb=" OH TYR D 77 " pdb=" OD2 ASP D 228 " model vdw 2.191 2.440 ... (remaining 74521 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' } 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 55 5.16 5 C 5855 2.51 5 N 1290 2.21 5 O 1470 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 Write .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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.980 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 25.210 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:10.840 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 8930 Z= 0.343 Angle : 0.896 17.694 12195 Z= 0.554 Chirality : 0.039 0.128 1370 Planarity : 0.004 0.026 1450 Dihedral : 13.622 119.814 2930 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1065 helix: 1.33 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -2.49 (0.37), residues: 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.943 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 209 average time/residue: 0.5662 time to fit residues: 133.9137 Evaluate side-chains 180 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1271 time to fit residues: 1.4397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 219 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 241 ASN C 177 ASN C 219 ASN D 219 ASN E 219 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8930 Z= 0.282 Angle : 0.515 8.928 12195 Z= 0.276 Chirality : 0.039 0.129 1370 Planarity : 0.004 0.032 1450 Dihedral : 11.446 110.141 1195 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1065 helix: 1.34 (0.16), residues: 935 sheet: None (None), residues: 0 loop : -2.11 (0.39), residues: 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 0.944 Fit side-chains outliers start: 36 outliers final: 22 residues processed: 199 average time/residue: 0.5962 time to fit residues: 133.6121 Evaluate side-chains 193 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 9 average time/residue: 0.2497 time to fit residues: 4.1421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 8930 Z= 0.233 Angle : 0.474 8.738 12195 Z= 0.255 Chirality : 0.037 0.127 1370 Planarity : 0.003 0.030 1450 Dihedral : 11.401 110.168 1195 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1065 helix: 1.40 (0.16), residues: 935 sheet: None (None), residues: 0 loop : -2.09 (0.41), residues: 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 0.951 Fit side-chains outliers start: 33 outliers final: 24 residues processed: 197 average time/residue: 0.6098 time to fit residues: 135.5853 Evaluate side-chains 199 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 10 average time/residue: 0.2472 time to fit residues: 4.4688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 101 optimal weight: 0.0010 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 30.0000 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8930 Z= 0.203 Angle : 0.451 5.850 12195 Z= 0.244 Chirality : 0.036 0.126 1370 Planarity : 0.003 0.029 1450 Dihedral : 11.329 109.674 1195 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 4.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1065 helix: 1.46 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -1.89 (0.41), residues: 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 0.934 Fit side-chains outliers start: 39 outliers final: 25 residues processed: 204 average time/residue: 0.5760 time to fit residues: 133.1452 Evaluate side-chains 202 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 9 average time/residue: 0.3376 time to fit residues: 4.8931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.1980 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8930 Z= 0.269 Angle : 0.501 6.371 12195 Z= 0.269 Chirality : 0.038 0.128 1370 Planarity : 0.004 0.031 1450 Dihedral : 11.252 109.626 1195 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 4.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1065 helix: 1.28 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -1.89 (0.42), residues: 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 0.970 Fit side-chains outliers start: 38 outliers final: 27 residues processed: 207 average time/residue: 0.5932 time to fit residues: 138.1802 Evaluate side-chains 210 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 18 residues processed: 11 average time/residue: 0.2829 time to fit residues: 5.1064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8930 Z= 0.192 Angle : 0.448 6.945 12195 Z= 0.244 Chirality : 0.036 0.125 1370 Planarity : 0.003 0.028 1450 Dihedral : 11.241 109.967 1195 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1065 helix: 1.48 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.92 (0.43), residues: 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 0.992 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 208 average time/residue: 0.5673 time to fit residues: 133.3182 Evaluate side-chains 203 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.4136 time to fit residues: 3.1840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 50.0000 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8930 Z= 0.238 Angle : 0.492 8.530 12195 Z= 0.264 Chirality : 0.037 0.127 1370 Planarity : 0.003 0.030 1450 Dihedral : 11.244 109.797 1195 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1065 helix: 1.40 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.95 (0.43), residues: 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 0.922 Fit side-chains outliers start: 32 outliers final: 24 residues processed: 201 average time/residue: 0.6128 time to fit residues: 138.6338 Evaluate side-chains 204 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 8 average time/residue: 0.2373 time to fit residues: 3.7164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 8930 Z= 0.284 Angle : 0.529 10.394 12195 Z= 0.281 Chirality : 0.038 0.133 1370 Planarity : 0.004 0.031 1450 Dihedral : 11.252 109.730 1195 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1065 helix: 1.26 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.99 (0.44), residues: 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 0.950 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 206 average time/residue: 0.6171 time to fit residues: 142.8319 Evaluate side-chains 206 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 8 average time/residue: 0.3629 time to fit residues: 4.6421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8930 Z= 0.239 Angle : 0.505 10.874 12195 Z= 0.269 Chirality : 0.037 0.137 1370 Planarity : 0.003 0.029 1450 Dihedral : 11.242 109.921 1195 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.24), residues: 1065 helix: 1.41 (0.16), residues: 915 sheet: None (None), residues: 0 loop : -1.34 (0.50), residues: 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 0.829 Fit side-chains outliers start: 23 outliers final: 21 residues processed: 200 average time/residue: 0.5792 time to fit residues: 131.1332 Evaluate side-chains 205 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 6 average time/residue: 0.2813 time to fit residues: 3.3767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 69 optimal weight: 0.0030 chunk 104 optimal weight: 4.9990 chunk 96 optimal weight: 0.0770 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.7752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8930 Z= 0.143 Angle : 0.441 11.925 12195 Z= 0.238 Chirality : 0.035 0.132 1370 Planarity : 0.003 0.027 1450 Dihedral : 11.254 110.217 1195 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1065 helix: 1.73 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.82 (0.47), residues: 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 0.749 Fit side-chains outliers start: 21 outliers final: 19 residues processed: 206 average time/residue: 0.5717 time to fit residues: 132.9447 Evaluate side-chains 198 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 4 average time/residue: 0.6223 time to fit residues: 4.0909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.166444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.142457 restraints weight = 9046.130| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.17 r_work: 0.3416 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.3318 rms_B_bonded: 2.65 restraints_weight: 0.1250 r_work: 0.3205 rms_B_bonded: 4.76 restraints_weight: 0.0625 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8930 Z= 0.153 Angle : 0.452 11.953 12195 Z= 0.243 Chirality : 0.035 0.128 1370 Planarity : 0.003 0.027 1450 Dihedral : 11.221 110.063 1195 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.25), residues: 1065 helix: 1.82 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.76 (0.47), residues: 140 =============================================================================== Job complete usr+sys time: 2365.89 seconds wall clock time: 43 minutes 18.17 seconds (2598.17 seconds total)