Starting phenix.real_space_refine on Wed May 8 23:32:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/05_2024/8hq7_34946.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/05_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_34946/05_2024/8hq7_34946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/05_2024/8hq7_34946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/05_2024/8hq7_34946.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hq7_34946/05_2024/8hq7_34946.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 4.98, per 1000 atoms: 0.60 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: 3.52 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: 1.16 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: 3.44 Time building geometry restraints manager: 3.69 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 2.440 nonbonded pdb=" OD2 ASP N 172 " pdb=" OG1 THR N 174 " model vdw 2.141 2.440 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 2.520 nonbonded pdb=" OG1 THR M 200 " pdb=" OE1 GLN M 201 " model vdw 2.301 2.440 ... (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 ========== 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: 7.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 33.540 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.300 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.600 ------------------------------------------------------------------------------- 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 : 1.008 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: 1.7295 time to fit residues: 213.6334 Evaluate side-chains 94 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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: 0.8227 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8493 Z= 0.293 Angle : 0.691 14.854 11560 Z= 0.359 Chirality : 0.047 0.234 1298 Planarity : 0.006 0.085 1487 Dihedral : 5.687 55.537 1209 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 1.50 % Allowed : 7.06 % Favored : 91.44 % 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: 0.13 (0.26), residues: 1072 helix: -2.70 (0.54), residues: 58 sheet: 1.43 (0.25), residues: 452 loop : -0.77 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 150 HIS 0.007 0.001 HIS A 519 PHE 0.012 0.001 PHE N 211 TYR 0.017 0.002 TYR N 194 ARG 0.005 0.000 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: 14 poor density : 92 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8256 (mttp) REVERT: M 208 ASN cc_start: 0.7168 (m-40) cc_final: 0.6963 (m110) REVERT: L 18 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7424 (ttm-80) REVERT: L 166 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5468 (pp20) outliers start: 14 outliers final: 3 residues processed: 99 average time/residue: 1.6040 time to fit residues: 167.2541 Evaluate side-chains 93 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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: 0.0040 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.0060 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 0.0570 chunk 77 optimal weight: 0.5980 overall best weight: 0.2926 ------------------------------------------------------------------------------- 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: 0.8163 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8493 Z= 0.140 Angle : 0.584 14.786 11560 Z= 0.302 Chirality : 0.044 0.216 1298 Planarity : 0.005 0.077 1487 Dihedral : 5.127 51.868 1209 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.18 % Allowed : 10.59 % Favored : 88.24 % 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: 0.34 (0.26), residues: 1072 helix: -2.44 (0.61), residues: 51 sheet: 1.44 (0.25), residues: 459 loop : -0.57 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 118 HIS 0.006 0.001 HIS A 519 PHE 0.007 0.001 PHE N 211 TYR 0.011 0.001 TYR H 160 ARG 0.003 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 101 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8227 (mttp) REVERT: M 82 MET cc_start: 0.9082 (mtp) cc_final: 0.8854 (mtp) REVERT: L 18 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7218 (ttm-80) outliers start: 11 outliers final: 0 residues processed: 97 average time/residue: 1.4699 time to fit residues: 149.8528 Evaluate side-chains 85 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: