Starting phenix.real_space_refine (version: dev) on Sun Feb 19 01:52:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2023/6tyi_20583_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2023/6tyi_20583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2023/6tyi_20583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2023/6tyi_20583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2023/6tyi_20583_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2023/6tyi_20583_updated.pdb" } resolution = 3.3 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= 0.008 sd= 0.148 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 GLU 64": "OE1" <-> "OE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E GLU 227": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9184 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 4, 'TRANS': 220} Chain: "C" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1712 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "D" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1712 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "E" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1696 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain: "Y" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 236 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "Z" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.65, per 1000 atoms: 0.62 Number of scatterers: 9184 At special positions: 0 Unit cell: (84.8, 84.8, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 4 15.00 O 1683 8.00 N 1567 7.00 C 5894 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 0 sheets defined 81.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 22 through 62 removed outlier: 4.514A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 83 through 97 Processing helix chain 'A' and resid 104 through 127 Processing helix chain 'A' and resid 130 through 158 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 177 through 232 Proline residue: A 190 - end of helix Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 21 through 64 removed outlier: 5.182A pdb=" N GLU B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 removed outlier: 5.423A pdb=" N ASP B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 97 removed outlier: 4.075A pdb=" N LEU B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 126 Processing helix chain 'B' and resid 130 through 161 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 171 through 232 removed outlier: 3.754A pdb=" N THR B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Proline residue: B 190 - end of helix Processing helix chain 'C' and resid 21 through 64 removed outlier: 4.454A pdb=" N GLU C 64 " --> pdb=" O GLN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 removed outlier: 5.382A pdb=" N ASP C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 97 Processing helix chain 'C' and resid 104 through 126 Processing helix chain 'C' and resid 129 through 162 removed outlier: 3.512A pdb=" N ILE C 136 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 139 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER C 140 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Proline residue: C 141 - end of helix removed outlier: 3.536A pdb=" N VAL C 149 " --> pdb=" O PHE C 146 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 162 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 231 Proline residue: C 190 - end of helix Processing helix chain 'D' and resid 12 through 15 No H-bonds generated for 'chain 'D' and resid 12 through 15' Processing helix chain 'D' and resid 22 through 64 removed outlier: 4.909A pdb=" N GLU D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 104 through 127 Processing helix chain 'D' and resid 130 through 160 Proline residue: D 141 - end of helix Processing helix chain 'D' and resid 171 through 232 removed outlier: 3.666A pdb=" N ALA D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 24 through 64 removed outlier: 4.278A pdb=" N GLY E 29 " --> pdb=" O CYS E 25 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 77 removed outlier: 5.054A pdb=" N ASP E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 104 through 126 Processing helix chain 'E' and resid 130 through 161 Proline residue: E 141 - end of helix removed outlier: 3.813A pdb=" N ALA E 160 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 232 removed outlier: 4.184A pdb=" N ILE E 189 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Proline residue: E 190 - end of helix removed outlier: 3.622A pdb=" N ILE E 194 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 21 through 36 removed outlier: 3.962A pdb=" N VAL Y 26 " --> pdb=" O PRO Y 22 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET Y 27 " --> pdb=" O PHE Y 23 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Y 29 " --> pdb=" O ASP Y 25 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU Y 31 " --> pdb=" O MET Y 27 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE Y 34 " --> pdb=" O LEU Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Z' and resid 24 through 38 removed outlier: 3.611A pdb=" N ILE Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL Z 36 " --> pdb=" O ILE Z 32 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA Z 38 " --> pdb=" O PHE Z 34 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2049 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: 2.51 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1524 1.30 - 1.43: 2284 1.43 - 1.55: 5412 1.55 - 1.68: 30 1.68 - 1.80: 67 Bond restraints: 9317 Sorted by residual: bond pdb=" C11 PGT A 301 " pdb=" O3 PGT A 301 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C31 PGT A 301 " pdb=" O2 PGT A 301 " ideal model delta sigma weight residual 1.331 1.404 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 PEV C 301 " pdb=" O2 PEV C 301 " ideal model delta sigma weight residual 1.330 1.403 -0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C31 PEV E 301 " pdb=" O2 PEV E 301 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C11 PEV C 301 " pdb=" O3 PEV C 301 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.83e+00 ... (remaining 9312 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.91: 118 105.91 - 112.95: 5301 112.95 - 119.99: 3453 119.99 - 127.02: 3627 127.02 - 134.06: 71 Bond angle restraints: 12570 Sorted by residual: angle pdb=" O3P PGT A 301 " pdb=" P PGT A 301 " pdb=" O4P PGT A 301 " ideal model delta sigma weight residual 92.82 111.48 -18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" O1P PEV C 301 " pdb=" P PEV C 301 " pdb=" O2P PEV C 301 " ideal model delta sigma weight residual 119.37 100.88 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" O3P PEV C 301 " pdb=" P PEV C 301 " pdb=" O4P PEV C 301 " ideal model delta sigma weight residual 93.57 111.90 -18.33 3.00e+00 1.11e-01 3.73e+01 angle pdb=" O1P PGT A 301 " pdb=" P PGT A 301 " pdb=" O2P PGT A 301 " ideal model delta sigma weight residual 119.10 100.80 18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" O3P PEV E 301 " pdb=" P PEV E 301 " pdb=" O4P PEV E 301 " ideal model delta sigma weight residual 93.57 111.77 -18.20 3.00e+00 1.11e-01 3.68e+01 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 4838 16.84 - 33.67: 535 33.67 - 50.51: 143 50.51 - 67.35: 32 67.35 - 84.19: 15 Dihedral angle restraints: 5563 sinusoidal: 2191 harmonic: 3372 Sorted by residual: dihedral pdb=" CA ALA A 19 " pdb=" C ALA A 19 " pdb=" N ASP A 20 " pdb=" CA ASP A 20 " ideal model delta harmonic sigma weight residual 180.00 -157.81 -22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ASP Z 17 " pdb=" C ASP Z 17 " pdb=" N ILE Z 18 " pdb=" CA ILE Z 18 " ideal model delta harmonic sigma weight residual -180.00 -163.78 -16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ALA E 19 " pdb=" C ALA E 19 " pdb=" N ASP E 20 " pdb=" CA ASP E 20 " ideal model delta harmonic sigma weight residual -180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 5560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 968 0.046 - 0.092: 424 0.092 - 0.138: 60 0.138 - 0.184: 10 0.184 - 0.230: 3 Chirality restraints: 1465 Sorted by residual: chirality pdb=" C5 PGT A 301 " pdb=" C4 PGT A 301 " pdb=" C6 PGT A 301 " pdb=" O5 PGT A 301 " both_signs ideal model delta sigma weight residual False -2.30 -2.53 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C2 PGT A 301 " pdb=" C1 PGT A 301 " pdb=" C3 PGT A 301 " pdb=" O2 PGT A 301 " both_signs ideal model delta sigma weight residual False 2.35 2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL B 197 " pdb=" CA VAL B 197 " pdb=" CG1 VAL B 197 " pdb=" CG2 VAL B 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1462 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 113 " 0.017 2.00e-02 2.50e+03 1.73e-02 5.26e+00 pdb=" CG PHE A 113 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 113 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 113 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 113 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 113 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 113 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 140 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 141 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 171 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO E 172 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 172 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 172 " -0.022 5.00e-02 4.00e+02 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 21 2.42 - 3.04: 6144 3.04 - 3.66: 13120 3.66 - 4.28: 19520 4.28 - 4.90: 32974 Nonbonded interactions: 71779 Sorted by model distance: nonbonded pdb=" OG SER D 98 " pdb=" NH1 ARG D 110 " model vdw 1.796 2.520 nonbonded pdb=" OG SER A 98 " pdb=" NH1 ARG A 110 " model vdw 2.179 2.520 nonbonded pdb=" OE2 GLU A 58 " pdb=" OG SER A 82 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR A 148 " pdb=" O ALA A 177 " model vdw 2.237 2.440 nonbonded pdb=" OE2 GLU B 58 " pdb=" OG SER B 82 " model vdw 2.241 2.440 ... (remaining 71774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 233) selection = (chain 'B' and resid 11 through 233) selection = (chain 'C' and resid 11 through 233) selection = (chain 'D' and resid 11 through 233) selection = (chain 'E' and resid 11 through 233) } ncs_group { reference = (chain 'Y' and resid 12 through 40) selection = chain 'Z' } 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 36 5.16 5 C 5894 2.51 5 N 1567 2.21 5 O 1683 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: 1.020 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: 0.030 Extract box with map and model: 2.680 Check model and map are aligned: 0.110 Process input model: 27.400 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.012 0.104 9317 Z= 0.758 Angle : 1.033 18.665 12570 Z= 0.504 Chirality : 0.049 0.230 1465 Planarity : 0.004 0.039 1598 Dihedral : 15.885 84.185 3385 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.14 % Rotamer Outliers : 0.43 % 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: -0.84 (0.22), residues: 1172 helix: 0.18 (0.15), residues: 996 sheet: None (None), residues: 0 loop : -4.46 (0.30), residues: 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 0.865 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 152 average time/residue: 0.2752 time to fit residues: 53.8715 Evaluate side-chains 115 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0771 time to fit residues: 1.6742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 104 ASN B 70 GLN B 93 ASN C 215 GLN D 93 ASN D 125 GLN D 163 GLN D 196 ASN E 69 ASN E 93 ASN E 154 ASN E 196 ASN Z 16 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9317 Z= 0.192 Angle : 0.519 7.638 12570 Z= 0.276 Chirality : 0.035 0.127 1465 Planarity : 0.005 0.030 1598 Dihedral : 9.488 57.524 1389 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 1.40 % 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: 1.63 (0.24), residues: 1172 helix: 1.90 (0.16), residues: 1004 sheet: None (None), residues: 0 loop : -4.24 (0.31), residues: 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.049 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 129 average time/residue: 0.3001 time to fit residues: 50.2675 Evaluate side-chains 112 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0994 time to fit residues: 2.2077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN E 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9317 Z= 0.214 Angle : 0.506 6.782 12570 Z= 0.262 Chirality : 0.035 0.119 1465 Planarity : 0.004 0.055 1598 Dihedral : 8.998 59.063 1389 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 1.83 % 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: 2.24 (0.25), residues: 1172 helix: 2.29 (0.16), residues: 1004 sheet: None (None), residues: 0 loop : -3.91 (0.33), residues: 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.042 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 130 average time/residue: 0.2587 time to fit residues: 44.6438 Evaluate side-chains 114 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1644 time to fit residues: 3.0321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.0980 chunk 99 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9317 Z= 0.170 Angle : 0.474 6.789 12570 Z= 0.247 Chirality : 0.035 0.177 1465 Planarity : 0.004 0.038 1598 Dihedral : 8.618 59.102 1389 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 1.29 % 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: 2.67 (0.25), residues: 1172 helix: 2.59 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -3.78 (0.33), residues: 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.910 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 120 average time/residue: 0.2623 time to fit residues: 41.9129 Evaluate side-chains 110 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0820 time to fit residues: 2.1664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9317 Z= 0.167 Angle : 0.478 6.763 12570 Z= 0.246 Chirality : 0.035 0.158 1465 Planarity : 0.004 0.026 1598 Dihedral : 8.352 59.914 1389 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 1.19 % 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: 2.85 (0.25), residues: 1172 helix: 2.69 (0.16), residues: 1004 sheet: None (None), residues: 0 loop : -3.60 (0.35), residues: 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.338 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 116 average time/residue: 0.2791 time to fit residues: 43.1121 Evaluate side-chains 110 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1267 time to fit residues: 2.2344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 9317 Z= 0.302 Angle : 0.563 7.796 12570 Z= 0.285 Chirality : 0.037 0.121 1465 Planarity : 0.004 0.030 1598 Dihedral : 8.587 58.294 1389 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.72 % 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: 2.52 (0.25), residues: 1172 helix: 2.45 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -3.56 (0.35), residues: 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.027 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 0.2447 time to fit residues: 42.4584 Evaluate side-chains 112 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0995 time to fit residues: 2.8383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN Z 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9317 Z= 0.235 Angle : 0.518 7.752 12570 Z= 0.266 Chirality : 0.036 0.130 1465 Planarity : 0.004 0.026 1598 Dihedral : 8.379 56.428 1389 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.65 % 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: 2.65 (0.25), residues: 1172 helix: 2.53 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -3.44 (0.36), residues: 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.899 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 115 average time/residue: 0.2692 time to fit residues: 41.1804 Evaluate side-chains 114 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1019 time to fit residues: 2.3988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9317 Z= 0.166 Angle : 0.484 8.293 12570 Z= 0.251 Chirality : 0.034 0.118 1465 Planarity : 0.004 0.025 1598 Dihedral : 7.967 55.011 1389 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.22 % 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: 2.94 (0.25), residues: 1172 helix: 2.74 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -3.37 (0.37), residues: 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.980 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.2891 time to fit residues: 40.3352 Evaluate side-chains 103 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 30.0000 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.0980 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9317 Z= 0.168 Angle : 0.482 8.254 12570 Z= 0.250 Chirality : 0.035 0.136 1465 Planarity : 0.004 0.025 1598 Dihedral : 7.693 58.400 1389 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.75 % 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: 3.04 (0.25), residues: 1172 helix: 2.79 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -3.24 (0.39), residues: 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.052 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 110 average time/residue: 0.2554 time to fit residues: 37.9098 Evaluate side-chains 106 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0971 time to fit residues: 1.7325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 0.0000 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9317 Z= 0.195 Angle : 0.499 8.355 12570 Z= 0.259 Chirality : 0.035 0.133 1465 Planarity : 0.004 0.027 1598 Dihedral : 7.550 55.246 1389 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.22 % 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: 3.03 (0.25), residues: 1172 helix: 2.78 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -3.22 (0.39), residues: 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.067 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 109 average time/residue: 0.2586 time to fit residues: 38.1355 Evaluate side-chains 106 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1091 time to fit residues: 1.7546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.162916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123990 restraints weight = 9429.765| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.94 r_work: 0.3211 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 9317 Z= 0.187 Angle : 0.495 8.171 12570 Z= 0.257 Chirality : 0.035 0.135 1465 Planarity : 0.004 0.035 1598 Dihedral : 7.418 55.580 1389 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.22 % 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: 3.07 (0.25), residues: 1172 helix: 2.80 (0.16), residues: 1001 sheet: None (None), residues: 0 loop : -3.18 (0.40), residues: 171 =============================================================================== Job complete usr+sys time: 1848.97 seconds wall clock time: 34 minutes 36.67 seconds (2076.67 seconds total)