Starting phenix.real_space_refine on Wed May 8 23:15:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpf_34931/05_2024/8hpf_34931.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpf_34931/05_2024/8hpf_34931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpf_34931/05_2024/8hpf_34931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpf_34931/05_2024/8hpf_34931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpf_34931/05_2024/8hpf_34931.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpf_34931/05_2024/8hpf_34931.pdb" } resolution = 2.34 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= -0.001 sd= 0.098 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 5217 2.51 5 N 1387 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 30": "OD1" <-> "OD2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "M TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "N TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "N PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 8268 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1542 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} 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: "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: "M" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.93, per 1000 atoms: 0.60 Number of scatterers: 8268 At special positions: 0 Unit cell: (110.04, 126, 120.96, 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 1630 8.00 N 1387 7.00 C 5217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 448 " distance=2.05 Simple disulfide: pdb=" SG CYS A 407 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 504 " 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 Simple disulfide: pdb=" SG CYS L 215 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 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 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 NAG-ASN " NAG A1201 " - " ASN A 359 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.6 seconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 10.0% alpha, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.677A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 removed outlier: 4.279A pdb=" N SER A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.558A pdb=" N SER A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) 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: 3.595A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 128 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'H' and resid 63 through 66 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 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 194 through 199 removed outlier: 4.030A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.082A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 374 Processing sheet with id=AA2, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.067A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.003A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER L 175 " --> pdb=" O THR L 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 146 through 151 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.495A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.566A pdb=" N PHE H 101 " --> pdb=" O TRP H 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.711A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.711A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.260A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.634A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE M 111 " --> pdb=" O ARG M 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.954A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.954A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 160 through 163 removed outlier: 4.638A pdb=" N TYR M 203 " --> pdb=" O VAL M 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.622A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.972A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.717A pdb=" N SER N 99 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 116 through 120 removed outlier: 5.778A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 147 through 152 367 hydrogen bonds defined for protein. 888 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: 2.68 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2661 1.36 - 1.49: 2300 1.49 - 1.62: 3471 1.62 - 1.75: 1 1.75 - 1.88: 40 Bond restraints: 8473 Sorted by residual: bond pdb=" CB PRO H 89 " pdb=" CG PRO H 89 " ideal model delta sigma weight residual 1.492 1.664 -0.172 5.00e-02 4.00e+02 1.19e+01 bond pdb=" C ASP H 116 " pdb=" N PRO H 117 " ideal model delta sigma weight residual 1.331 1.367 -0.036 1.27e-02 6.20e+03 8.21e+00 bond pdb=" CG PRO H 89 " pdb=" CD PRO H 89 " ideal model delta sigma weight residual 1.503 1.414 0.089 3.40e-02 8.65e+02 6.91e+00 bond pdb=" N PRO H 89 " pdb=" CD PRO H 89 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.67e+00 bond pdb=" N PRO H 89 " pdb=" CA PRO H 89 " ideal model delta sigma weight residual 1.469 1.440 0.028 1.28e-02 6.10e+03 4.87e+00 ... (remaining 8468 not shown) Histogram of bond angle deviations from ideal: 94.34 - 102.28: 14 102.28 - 110.21: 1758 110.21 - 118.15: 4670 118.15 - 126.09: 4950 126.09 - 134.03: 140 Bond angle restraints: 11532 Sorted by residual: angle pdb=" CA PRO H 89 " pdb=" N PRO H 89 " pdb=" CD PRO H 89 " ideal model delta sigma weight residual 112.00 94.34 17.66 1.40e+00 5.10e-01 1.59e+02 angle pdb=" CA CYS A 448 " pdb=" CB CYS A 448 " pdb=" SG CYS A 448 " ideal model delta sigma weight residual 114.40 128.38 -13.98 2.30e+00 1.89e-01 3.69e+01 angle pdb=" N PRO H 89 " pdb=" CD PRO H 89 " pdb=" CG PRO H 89 " ideal model delta sigma weight residual 103.20 94.70 8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" C GLU M 157 " pdb=" N PRO M 158 " pdb=" CD PRO M 158 " ideal model delta sigma weight residual 120.60 108.52 12.08 2.20e+00 2.07e-01 3.01e+01 angle pdb=" C GLY A 447 " pdb=" N CYS A 448 " pdb=" CA CYS A 448 " ideal model delta sigma weight residual 122.09 114.51 7.58 1.86e+00 2.89e-01 1.66e+01 ... (remaining 11527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4326 17.31 - 34.61: 509 34.61 - 51.92: 178 51.92 - 69.22: 47 69.22 - 86.53: 16 Dihedral angle restraints: 5076 sinusoidal: 1959 harmonic: 3117 Sorted by residual: dihedral pdb=" CB CYS A 395 " pdb=" SG CYS A 395 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual 93.00 20.69 72.31 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CB CYS N 136 " pdb=" SG CYS N 136 " pdb=" SG CYS N 196 " pdb=" CB CYS N 196 " ideal model delta sinusoidal sigma weight residual 93.00 45.14 47.86 1 1.00e+01 1.00e-02 3.16e+01 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 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1038 0.050 - 0.099: 186 0.099 - 0.149: 59 0.149 - 0.198: 3 0.198 - 0.248: 2 Chirality restraints: 1288 Sorted by residual: chirality pdb=" CA PRO H 89 " pdb=" N PRO H 89 " pdb=" C PRO H 89 " pdb=" CB PRO H 89 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C1 NAG A1201 " pdb=" ND2 ASN A 359 " pdb=" C2 NAG A1201 " pdb=" O5 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA THR N 94 " pdb=" N THR N 94 " pdb=" C THR N 94 " pdb=" CB THR N 94 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 1285 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 88 " 0.089 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO H 89 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO H 89 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 89 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 157 " -0.078 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO M 158 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 94 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO N 95 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO N 95 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 95 " -0.040 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1502 2.78 - 3.31: 7347 3.31 - 3.84: 14187 3.84 - 4.37: 16529 4.37 - 4.90: 28271 Nonbonded interactions: 67836 Sorted by model distance: nonbonded pdb=" O HIS N 191 " pdb=" NH2 ARG N 213 " model vdw 2.244 2.520 nonbonded pdb=" OD2 ASP A 436 " pdb=" OG SER M 56 " model vdw 2.247 2.440 nonbonded pdb=" N ASN A 503 " pdb=" OD1 ASN A 503 " model vdw 2.267 2.520 nonbonded pdb=" O SER H 128 " pdb=" OG SER H 128 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR H 110 " pdb=" OG SER H 113 " model vdw 2.277 2.440 ... (remaining 67831 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: 0.010 Normalize map: mean=0, sd=1: 25.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 28.590 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.560 Find NCS groups from input model: 0.320 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 0.172 8473 Z= 0.214 Angle : 0.684 17.663 11532 Z= 0.359 Chirality : 0.044 0.248 1288 Planarity : 0.007 0.120 1484 Dihedral : 17.785 86.530 3042 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 7.09 % Allowed : 26.42 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.27), residues: 1069 helix: -1.87 (0.76), residues: 33 sheet: 0.96 (0.25), residues: 439 loop : -0.71 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 149 HIS 0.008 0.001 HIS L 199 PHE 0.023 0.001 PHE L 117 TYR 0.015 0.001 TYR H 111 ARG 0.011 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 92 time to evaluate : 0.748 Fit side-chains outliers start: 66 outliers final: 56 residues processed: 156 average time/residue: 0.8477 time to fit residues: 143.9302 Evaluate side-chains 139 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 83 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 54 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN N 139 ASN N 162 GLN ** N 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8473 Z= 0.336 Angle : 0.698 13.964 11532 Z= 0.360 Chirality : 0.047 0.251 1288 Planarity : 0.007 0.095 1484 Dihedral : 10.204 78.677 1260 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 9.34 % Allowed : 23.85 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: 1069 helix: -2.01 (0.69), residues: 41 sheet: 0.96 (0.25), residues: 434 loop : -0.98 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 163 HIS 0.008 0.002 HIS N 191 PHE 0.013 0.002 PHE M 175 TYR 0.020 0.002 TYR N 188 ARG 0.006 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 91 time to evaluate : 0.990 Fit side-chains REVERT: L 30 ASP cc_start: 0.7208 (t0) cc_final: 0.6928 (t0) REVERT: N 61 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7044 (ptt-90) outliers start: 87 outliers final: 47 residues processed: 170 average time/residue: 0.8700 time to fit residues: 161.1414 Evaluate side-chains 138 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 90 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 139 ASN Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 chunk 95 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN N 162 GLN N 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8473 Z= 0.179 Angle : 0.621 13.920 11532 Z= 0.316 Chirality : 0.044 0.237 1288 Planarity : 0.006 0.084 1484 Dihedral : 8.689 77.494 1225 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 7.20 % Allowed : 26.53 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.17 (0.26), residues: 1069 helix: -1.89 (0.69), residues: 41 sheet: 1.04 (0.26), residues: 424 loop : -0.86 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 163 HIS 0.004 0.001 HIS L 199 PHE 0.015 0.001 PHE H 137 TYR 0.015 0.001 TYR N 188 ARG 0.006 0.000 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 96 time to evaluate : 0.928 Fit side-chains REVERT: L 30 ASP cc_start: 0.7159 (t0) cc_final: 0.6880 (t0) REVERT: M 210 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6201 (pttt) REVERT: N 61 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7021 (ptt-90) outliers start: 67 outliers final: 41 residues processed: 158 average time/residue: 0.9867 time to fit residues: 168.5304 Evaluate side-chains 131 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 88 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN L 156 GLN N 37 GLN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN N 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8473 Z= 0.281 Angle : 0.674 14.725 11532 Z= 0.345 Chirality : 0.046 0.255 1288 Planarity : 0.006 0.087 1484 Dihedral : 8.705 78.922 1219 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 7.84 % Allowed : 26.42 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.33 (0.26), residues: 1069 helix: -1.92 (0.70), residues: 41 sheet: 0.87 (0.25), residues: 433 loop : -0.95 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 163 HIS 0.006 0.002 HIS N 191 PHE 0.015 0.002 PHE L 117 TYR 0.021 0.002 TYR N 188 ARG 0.006 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 92 time to evaluate : 0.902 Fit side-chains REVERT: A 394 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7384 (ptpp) REVERT: M 210 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6369 (pttt) REVERT: N 61 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7055 (ptt-90) outliers start: 73 outliers final: 45 residues processed: 158 average time/residue: 0.9176 time to fit residues: 157.3100 Evaluate side-chains 136 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 88 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 0.0070 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN N 157 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8473 Z= 0.166 Angle : 0.618 13.057 11532 Z= 0.313 Chirality : 0.044 0.226 1288 Planarity : 0.006 0.079 1484 Dihedral : 7.664 77.146 1217 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 6.55 % Allowed : 27.18 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 (0.27), residues: 1069 helix: -1.90 (0.73), residues: 34 sheet: 1.01 (0.25), residues: 427 loop : -0.80 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 163 HIS 0.005 0.001 HIS L 199 PHE 0.012 0.001 PHE N 141 TYR 0.014 0.001 TYR N 188 ARG 0.006 0.000 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 92 time to evaluate : 0.901 Fit side-chains REVERT: A 394 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7229 (ptpp) REVERT: L 30 ASP cc_start: 0.7203 (t0) cc_final: 0.6873 (t0) REVERT: L 136 LEU cc_start: 0.5659 (OUTLIER) cc_final: 0.5263 (tp) REVERT: L 208 LYS cc_start: 0.3871 (OUTLIER) cc_final: 0.3561 (pttp) REVERT: M 210 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6156 (pttt) outliers start: 61 outliers final: 27 residues processed: 149 average time/residue: 0.9456 time to fit residues: 152.5182 Evaluate side-chains 120 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN N 37 GLN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 8473 Z= 0.428 Angle : 0.766 15.518 11532 Z= 0.394 Chirality : 0.049 0.280 1288 Planarity : 0.007 0.089 1484 Dihedral : 8.381 79.902 1206 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 7.41 % Allowed : 26.21 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.57 (0.26), residues: 1069 helix: -2.01 (0.70), residues: 41 sheet: 0.67 (0.25), residues: 430 loop : -1.08 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 163 HIS 0.010 0.002 HIS N 191 PHE 0.015 0.003 PHE M 175 TYR 0.025 0.002 TYR N 188 ARG 0.007 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 87 time to evaluate : 0.969 Fit side-chains REVERT: L 136 LEU cc_start: 0.5705 (OUTLIER) cc_final: 0.5315 (tp) REVERT: H 190 LEU cc_start: 0.4144 (OUTLIER) cc_final: 0.3894 (tt) REVERT: M 204 ILE cc_start: 0.5099 (pp) cc_final: 0.4785 (pt) REVERT: M 210 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6290 (pttt) REVERT: M 218 LYS cc_start: 0.4372 (OUTLIER) cc_final: 0.3599 (mmmm) outliers start: 69 outliers final: 38 residues processed: 150 average time/residue: 0.7941 time to fit residues: 128.9741 Evaluate side-chains 126 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 84 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN N 37 GLN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN ** N 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8473 Z= 0.242 Angle : 0.675 14.324 11532 Z= 0.344 Chirality : 0.046 0.255 1288 Planarity : 0.006 0.084 1484 Dihedral : 8.035 78.575 1206 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.16 % Allowed : 28.79 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.42 (0.26), residues: 1069 helix: -1.88 (0.76), residues: 33 sheet: 0.74 (0.25), residues: 430 loop : -0.97 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 149 HIS 0.007 0.001 HIS L 199 PHE 0.016 0.002 PHE H 137 TYR 0.023 0.002 TYR N 188 ARG 0.007 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 89 time to evaluate : 0.697 Fit side-chains REVERT: H 190 LEU cc_start: 0.4205 (OUTLIER) cc_final: 0.3907 (tt) REVERT: M 204 ILE cc_start: 0.5003 (pp) cc_final: 0.4694 (pt) REVERT: M 210 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6322 (pttt) REVERT: N 124 ASP cc_start: 0.4521 (OUTLIER) cc_final: 0.3607 (m-30) outliers start: 48 outliers final: 34 residues processed: 133 average time/residue: 0.6539 time to fit residues: 94.6888 Evaluate side-chains 121 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 84 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 193 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 chunk 89 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: