Starting phenix.real_space_refine on Sun Aug 4 17:12:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/08_2024/8hq7_34946.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/08_2024/8hq7_34946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/08_2024/8hq7_34946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/08_2024/8hq7_34946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/08_2024/8hq7_34946.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/08_2024/8hq7_34946.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3142 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5221 2.51 5 N 1387 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "M GLU 1": "OE1" <-> "OE2" Residue "M GLU 26": "OE1" <-> "OE2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 172": "OD1" <-> "OD2" Residue "N PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 94": "OD1" <-> "OD2" Residue "L PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8292 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "M" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.35, per 1000 atoms: 0.77 Number of scatterers: 8292 At special positions: 0 Unit cell: (136.96, 93.304, 124.12, 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 34 16.00 O 1650 8.00 N 1387 7.00 C 5221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.04 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS H 231 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.6 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 9.7% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.709A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.957A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.428A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 165 through 167 No H-bonds generated for 'chain 'M' and resid 165 through 167' Processing helix chain 'M' and resid 194 through 199 removed outlier: 4.071A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.233A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 129 removed outlier: 4.058A pdb=" N SER N 129 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 190 removed outlier: 3.988A pdb=" N LYS N 190 " --> pdb=" O ALA N 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.560A pdb=" N ASN H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN H 67 " --> pdb=" O SER H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 67' Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.160A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.089A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.089A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE M 111 " --> pdb=" O ARG M 97 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N SER M 99 " --> pdb=" O PHE M 109 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE M 109 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 129 through 133 removed outlier: 6.023A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 129 through 133 removed outlier: 6.023A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 160 through 163 Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.574A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.942A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 13 removed outlier: 4.014A pdb=" N SER N 99 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 116 through 120 removed outlier: 6.137A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 155 through 156 Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.171A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.529A pdb=" N PHE H 101 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE H 115 " --> pdb=" O PHE H 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.413A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.413A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER H 192 " --> pdb=" O VAL H 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.849A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.989A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.915A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 146 through 151 361 hydrogen bonds defined for protein. 891 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: 2.64 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2658 1.35 - 1.47: 2174 1.47 - 1.59: 3621 1.59 - 1.71: 0 1.71 - 1.83: 40 Bond restraints: 8493 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " ideal model delta sigma weight residual 1.534 1.512 0.022 1.78e-02 3.16e+03 1.50e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C3 NAG B 2 " pdb=" O3 NAG B 2 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 8488 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.21: 305 107.21 - 113.95: 4732 113.95 - 120.70: 3171 120.70 - 127.44: 3264 127.44 - 134.18: 88 Bond angle restraints: 11560 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 134.18 -19.78 2.30e+00 1.89e-01 7.40e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 133.94 -19.54 2.30e+00 1.89e-01 7.22e+01 angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 108.99 117.53 -8.54 1.57e+00 4.06e-01 2.96e+01 angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 108.60 115.16 -6.56 1.46e+00 4.69e-01 2.02e+01 angle pdb=" C PRO H 14 " pdb=" N THR H 15 " pdb=" CA THR H 15 " ideal model delta sigma weight residual 122.08 127.66 -5.58 1.47e+00 4.63e-01 1.44e+01 ... (remaining 11555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 4661 16.21 - 32.42: 331 32.42 - 48.62: 80 48.62 - 64.83: 20 64.83 - 81.04: 12 Dihedral angle restraints: 5104 sinusoidal: 1980 harmonic: 3124 Sorted by residual: dihedral pdb=" CA ASP H 116 " pdb=" C ASP H 116 " pdb=" N PRO H 117 " pdb=" CA PRO H 117 " ideal model delta harmonic sigma weight residual 180.00 -130.92 -49.08 0 5.00e+00 4.00e-02 9.64e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -4.96 -81.04 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS M 149 " pdb=" SG CYS M 149 " pdb=" SG CYS M 205 " pdb=" CB CYS M 205 " ideal model delta sinusoidal sigma weight residual 93.00 173.58 -80.58 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 5101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1181 0.083 - 0.167: 114 0.167 - 0.250: 1 0.250 - 0.333: 1 0.333 - 0.417: 1 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CA CYS A 379 " pdb=" N CYS A 379 " pdb=" C CYS A 379 " pdb=" CB CYS A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA THR H 15 " pdb=" N THR H 15 " pdb=" C THR H 15 " pdb=" CB THR H 15 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1295 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 116 " 0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO H 117 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO H 117 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO H 117 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 157 " 0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO M 158 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 80 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO L 81 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 81 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 81 " 0.027 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 141 2.68 - 3.24: 7354 3.24 - 3.79: 12087 3.79 - 4.35: 16965 4.35 - 4.90: 28668 Nonbonded interactions: 65215 Sorted by model distance: nonbonded pdb=" OG SER L 163 " pdb=" OG SER L 177 " model vdw 2.131 3.040 nonbonded pdb=" OD2 ASP N 172 " pdb=" OG1 THR N 174 " model vdw 2.141 3.040 nonbonded pdb=" CB CYS A 379 " pdb=" CB CYS A 432 " model vdw 2.212 3.072 nonbonded pdb=" OD1 ASP M 61 " pdb=" NH2 ARG N 96 " model vdw 2.291 3.120 nonbonded pdb=" OG1 THR M 200 " pdb=" OE1 GLN M 201 " model vdw 2.301 3.040 ... (remaining 65210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.300 Process input model: 27.670 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.003 0.033 8493 Z= 0.223 Angle : 0.720 19.780 11560 Z= 0.372 Chirality : 0.047 0.417 1298 Planarity : 0.006 0.086 1487 Dihedral : 12.536 77.415 3066 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: 0.23 (0.26), residues: 1072 helix: -2.67 (0.55), residues: 57 sheet: 1.41 (0.25), residues: 452 loop : -0.61 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 118 HIS 0.004 0.001 HIS N 191 PHE 0.011 0.001 PHE N 211 TYR 0.015 0.002 TYR H 160 ARG 0.004 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: M 208 ASN cc_start: 0.7153 (m110) cc_final: 0.6844 (m110) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 1.6469 time to fit residues: 203.7904 Evaluate side-chains 94 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS M 13 GLN M 208 ASN N 162 GLN N 191 HIS H 212 ASN L 125 GLN ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8493 Z= 0.311 Angle : 0.709 14.932 11560 Z= 0.369 Chirality : 0.048 0.237 1298 Planarity : 0.006 0.086 1487 Dihedral : 5.734 55.317 1209 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 1.39 % Allowed : 6.84 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.12 (0.26), residues: 1072 helix: -2.79 (0.51), residues: 58 sheet: 1.42 (0.25), residues: 449 loop : -0.75 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 150 HIS 0.006 0.001 HIS A 519 PHE 0.012 0.001 PHE N 211 TYR 0.017 0.002 TYR N 194 ARG 0.005 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8258 (mttp) REVERT: M 215 LYS cc_start: 0.5391 (mmtm) cc_final: 0.4891 (tptt) REVERT: L 18 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7426 (ttm-80) REVERT: L 166 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5653 (pp20) outliers start: 13 outliers final: 3 residues processed: 100 average time/residue: 1.5102 time to fit residues: 158.8156 Evaluate side-chains 92 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 166 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS N 162 GLN N 191 HIS ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8493 Z= 0.188 Angle : 0.625 15.755 11560 Z= 0.325 Chirality : 0.045 0.226 1298 Planarity : 0.005 0.080 1487 Dihedral : 5.317 52.196 1209 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.50 % Allowed : 10.48 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.22 (0.26), residues: 1072 helix: -2.88 (0.53), residues: 57 sheet: 1.40 (0.25), residues: 464 loop : -0.65 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.007 0.001 HIS A 519 PHE 0.009 0.001 PHE N 211 TYR 0.013 0.001 TYR H 160 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8222 (mttp) REVERT: M 215 LYS cc_start: 0.5283 (mmtm) cc_final: 0.4849 (tptt) REVERT: L 18 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7369 (ttm-80) outliers start: 14 outliers final: 4 residues processed: 96 average time/residue: 1.5611 time to fit residues: 157.6324 Evaluate side-chains 89 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8493 Z= 0.217 Angle : 0.639 12.927 11560 Z= 0.333 Chirality : 0.045 0.212 1298 Planarity : 0.005 0.080 1487 Dihedral : 5.222 48.556 1209 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.46 % Allowed : 11.66 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.24 (0.26), residues: 1072 helix: -2.58 (0.58), residues: 51 sheet: 1.48 (0.25), residues: 450 loop : -0.70 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 118 HIS 0.008 0.001 HIS A 519 PHE 0.010 0.001 PHE L 119 TYR 0.014 0.002 TYR H 109 ARG 0.005 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8258 (mttp) REVERT: M 215 LYS cc_start: 0.5264 (mmtm) cc_final: 0.4845 (tptt) REVERT: N 79 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: H 91 ASP cc_start: 0.7847 (m-30) cc_final: 0.7633 (m-30) REVERT: L 78 ARG cc_start: 0.6568 (mmm160) cc_final: 0.5782 (tpt-90) REVERT: L 166 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5276 (pp20) outliers start: 23 outliers final: 6 residues processed: 101 average time/residue: 1.4013 time to fit residues: 149.4206 Evaluate side-chains 90 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 166 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 0.0370 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.0370 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8493 Z= 0.179 Angle : 0.611 15.788 11560 Z= 0.317 Chirality : 0.045 0.251 1298 Planarity : 0.005 0.076 1487 Dihedral : 4.952 47.116 1209 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.93 % Allowed : 13.05 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.29 (0.26), residues: 1072 helix: -2.84 (0.53), residues: 57 sheet: 1.56 (0.25), residues: 449 loop : -0.63 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.008 0.001 HIS A 519 PHE 0.009 0.001 PHE N 211 TYR 0.011 0.001 TYR H 160 ARG 0.004 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8228 (mttp) REVERT: M 215 LYS cc_start: 0.5188 (mmtm) cc_final: 0.4865 (tptt) REVERT: L 18 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7193 (ttm-80) REVERT: L 78 ARG cc_start: 0.6604 (mmm160) cc_final: 0.5828 (tpt-90) REVERT: L 166 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5226 (pp20) outliers start: 18 outliers final: 4 residues processed: 94 average time/residue: 1.4772 time to fit residues: 146.4762 Evaluate side-chains 86 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 166 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8493 Z= 0.172 Angle : 0.601 13.953 11560 Z= 0.312 Chirality : 0.044 0.239 1298 Planarity : 0.005 0.075 1487 Dihedral : 4.697 46.174 1209 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.03 % Allowed : 13.58 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.35 (0.26), residues: 1072 helix: -2.80 (0.54), residues: 57 sheet: 1.73 (0.26), residues: 428 loop : -0.64 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.008 0.001 HIS A 519 PHE 0.009 0.001 PHE N 211 TYR 0.011 0.001 TYR H 96 ARG 0.003 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8232 (mttp) REVERT: M 215 LYS cc_start: 0.5135 (mmtm) cc_final: 0.4847 (tptt) REVERT: H 91 ASP cc_start: 0.7713 (m-30) cc_final: 0.7444 (m-30) REVERT: L 78 ARG cc_start: 0.6579 (mmm160) cc_final: 0.6263 (tmt170) REVERT: L 166 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5236 (pp20) outliers start: 19 outliers final: 5 residues processed: 95 average time/residue: 1.5362 time to fit residues: 153.9177 Evaluate side-chains 86 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 166 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 0.0000 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8493 Z= 0.183 Angle : 0.613 16.242 11560 Z= 0.317 Chirality : 0.045 0.255 1298 Planarity : 0.005 0.075 1487 Dihedral : 4.654 46.391 1209 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.03 % Allowed : 14.12 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.32 (0.26), residues: 1072 helix: -2.80 (0.55), residues: 57 sheet: 1.72 (0.26), residues: 428 loop : -0.66 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 118 HIS 0.009 0.001 HIS A 519 PHE 0.009 0.001 PHE N 211 TYR 0.012 0.001 TYR H 96 ARG 0.003 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8240 (mttp) REVERT: M 215 LYS cc_start: 0.5220 (mmtm) cc_final: 0.4888 (tptt) REVERT: H 16 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.6294 (mp10) REVERT: L 78 ARG cc_start: 0.6604 (mmm160) cc_final: 0.6300 (tmt170) REVERT: L 166 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5249 (pp20) outliers start: 19 outliers final: 9 residues processed: 95 average time/residue: 1.5461 time to fit residues: 154.5659 Evaluate side-chains 93 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 166 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.0050 chunk 19 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8493 Z= 0.165 Angle : 0.602 15.109 11560 Z= 0.312 Chirality : 0.044 0.253 1298 Planarity : 0.005 0.073 1487 Dihedral : 4.552 45.138 1209 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.82 % Allowed : 14.76 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.37 (0.26), residues: 1072 helix: -2.77 (0.55), residues: 57 sheet: 1.76 (0.26), residues: 428 loop : -0.63 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.010 0.001 HIS A 519 PHE 0.009 0.001 PHE N 211 TYR 0.010 0.001 TYR H 96 ARG 0.003 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8234 (mttp) REVERT: M 215 LYS cc_start: 0.5185 (mmtm) cc_final: 0.4895 (tptt) REVERT: H 16 GLN cc_start: 0.6722 (OUTLIER) cc_final: 0.6383 (mp10) REVERT: L 78 ARG cc_start: 0.6590 (mmm160) cc_final: 0.5885 (tpt-90) REVERT: L 166 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5503 (pp20) outliers start: 17 outliers final: 8 residues processed: 97 average time/residue: 1.5098 time to fit residues: 154.2238 Evaluate side-chains 92 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 166 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8156 > 50: distance: 0 - 1: 8.738 distance: 2 - 3: 15.457 distance: 2 - 8: 5.591 distance: 4 - 5: 5.480 distance: 5 - 6: 6.271 distance: 5 - 7: 7.968 distance: 8 - 9: 28.053 distance: 9 - 10: 46.495 distance: 9 - 12: 12.693 distance: 10 - 11: 42.381 distance: 10 - 16: 39.228 distance: 12 - 13: 6.952 distance: 12 - 14: 33.044 distance: 13 - 15: 21.989 distance: 16 - 17: 15.624 distance: 17 - 18: 10.594 distance: 17 - 20: 15.023 distance: 18 - 19: 32.482 distance: 18 - 25: 21.346 distance: 20 - 21: 9.643 distance: 21 - 22: 16.125 distance: 22 - 23: 9.524 distance: 22 - 24: 13.384 distance: 25 - 26: 29.104 distance: 26 - 27: 6.984 distance: 26 - 29: 7.504 distance: 27 - 28: 23.093 distance: 27 - 33: 16.620 distance: 29 - 30: 38.488 distance: 30 - 31: 36.551 distance: 31 - 32: 46.984 distance: 33 - 34: 20.682 distance: 33 - 102: 16.080 distance: 34 - 35: 13.050 distance: 34 - 37: 17.458 distance: 35 - 36: 16.842 distance: 35 - 40: 14.157 distance: 36 - 99: 25.504 distance: 37 - 38: 27.151 distance: 37 - 39: 22.430 distance: 40 - 41: 16.131 distance: 41 - 42: 19.609 distance: 41 - 44: 32.675 distance: 42 - 43: 17.714 distance: 42 - 49: 21.952 distance: 44 - 45: 11.076 distance: 45 - 46: 17.223 distance: 46 - 47: 18.851 distance: 46 - 48: 28.333 distance: 49 - 50: 37.074 distance: 49 - 89: 30.976 distance: 50 - 51: 27.669 distance: 50 - 53: 39.181 distance: 51 - 52: 42.401 distance: 51 - 55: 23.203 distance: 52 - 86: 32.983 distance: 53 - 54: 10.309 distance: 55 - 56: 38.482 distance: 55 - 61: 12.341 distance: 56 - 57: 11.988 distance: 56 - 59: 20.248 distance: 57 - 58: 41.213 distance: 57 - 62: 33.056 distance: 59 - 60: 8.131 distance: 60 - 61: 28.159 distance: 62 - 63: 27.188 distance: 63 - 64: 11.905 distance: 63 - 66: 29.750 distance: 64 - 68: 34.901 distance: 66 - 67: 19.663