Starting phenix.real_space_refine on Fri Aug 2 19:22:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc1_39919/08_2024/8zc1_39919.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc1_39919/08_2024/8zc1_39919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc1_39919/08_2024/8zc1_39919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc1_39919/08_2024/8zc1_39919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc1_39919/08_2024/8zc1_39919.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc1_39919/08_2024/8zc1_39919.cif" } resolution = 4.17 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2907 2.51 5 N 767 2.21 5 O 878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4570 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1318 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 9, 'TRANS': 153} Chain breaks: 2 Chain: "C" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.52, per 1000 atoms: 0.77 Number of scatterers: 4570 At special positions: 0 Unit cell: (84.48, 76.56, 120.12, 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 18 16.00 O 878 8.00 N 767 7.00 C 2907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 210 " distance=2.03 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 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 723.2 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 15 sheets defined 6.9% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.145A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.518A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.669A pdb=" N GLN C 137 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.635A pdb=" N TRP C 196 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS C 197 " --> pdb=" O PRO C 193 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 192 through 199' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.894A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 removed outlier: 4.025A pdb=" N TRP E 111 " --> pdb=" O CYS E 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.810A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.864A pdb=" N ASP C 86 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 12 Processing sheet with id=AA5, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 129 removed outlier: 3.684A pdb=" N THR C 127 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 146 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 129 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL C 144 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 185 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP C 149 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR C 183 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 188 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C 171 " --> pdb=" O TYR C 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.804A pdb=" N ALA C 184 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 164 through 166 removed outlier: 4.451A pdb=" N TRP C 159 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 156 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 166 removed outlier: 4.451A pdb=" N TRP C 159 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 156 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 202 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 215 " --> pdb=" O CYS C 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.615A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 5 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 20 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 4.109A pdb=" N ASN E 59 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP E 50 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N CYS E 96 " --> pdb=" O TRP E 117 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TRP E 117 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG E 98 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 4.109A pdb=" N ASN E 59 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP E 50 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 137 removed outlier: 3.631A pdb=" N SER E 134 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER E 194 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL E 195 " --> pdb=" O HIS E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 137 removed outlier: 3.631A pdb=" N SER E 134 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER E 194 " --> pdb=" O CYS E 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 166 through 168 removed outlier: 4.071A pdb=" N CYS E 210 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 223 " --> pdb=" O CYS E 210 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 330 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: 1.20 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1449 1.35 - 1.47: 1259 1.47 - 1.59: 1964 1.59 - 1.71: 0 1.71 - 1.84: 22 Bond restraints: 4694 Sorted by residual: bond pdb=" C LYS E 215 " pdb=" N PRO E 216 " ideal model delta sigma weight residual 1.335 1.382 -0.046 1.30e-02 5.92e+03 1.28e+01 bond pdb=" C VAL B 382 " pdb=" N SER B 383 " ideal model delta sigma weight residual 1.327 1.288 0.039 1.71e-02 3.42e+03 5.13e+00 bond pdb=" N ASP E 158 " pdb=" CA ASP E 158 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.46e+00 bond pdb=" CA THR E 77 " pdb=" CB THR E 77 " ideal model delta sigma weight residual 1.527 1.554 -0.027 1.70e-02 3.46e+03 2.45e+00 bond pdb=" C PHE E 136 " pdb=" N PRO E 137 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.25e-02 6.40e+03 1.60e+00 ... (remaining 4689 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.29: 207 107.29 - 113.99: 2525 113.99 - 120.68: 1761 120.68 - 127.38: 1835 127.38 - 134.08: 70 Bond angle restraints: 6398 Sorted by residual: angle pdb=" C ILE E 76 " pdb=" N THR E 77 " pdb=" CA THR E 77 " ideal model delta sigma weight residual 122.46 128.09 -5.63 1.41e+00 5.03e-01 1.60e+01 angle pdb=" C LYS C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C VAL E 125 " pdb=" N SER E 126 " pdb=" CA SER E 126 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" CA THR E 77 " pdb=" CB THR E 77 " pdb=" CG2 THR E 77 " ideal model delta sigma weight residual 110.50 115.72 -5.22 1.70e+00 3.46e-01 9.42e+00 angle pdb=" CG1 ILE E 76 " pdb=" CB ILE E 76 " pdb=" CG2 ILE E 76 " ideal model delta sigma weight residual 110.70 102.26 8.44 3.00e+00 1.11e-01 7.92e+00 ... (remaining 6393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 2502 16.06 - 32.12: 205 32.12 - 48.19: 47 48.19 - 64.25: 10 64.25 - 80.31: 9 Dihedral angle restraints: 2773 sinusoidal: 1047 harmonic: 1726 Sorted by residual: dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 210 " pdb=" CB CYS E 210 " ideal model delta sinusoidal sigma weight residual 93.00 166.07 -73.07 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 53.44 39.56 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 130.42 -37.42 1 1.00e+01 1.00e-02 1.98e+01 ... (remaining 2770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 514 0.053 - 0.105: 149 0.105 - 0.158: 35 0.158 - 0.210: 1 0.210 - 0.263: 2 Chirality restraints: 701 Sorted by residual: chirality pdb=" CB VAL E 125 " pdb=" CA VAL E 125 " pdb=" CG1 VAL E 125 " pdb=" CG2 VAL E 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE E 76 " pdb=" CA ILE E 76 " pdb=" CG1 ILE E 76 " pdb=" CG2 ILE E 76 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA THR E 77 " pdb=" N THR E 77 " pdb=" C THR E 77 " pdb=" CB THR E 77 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 698 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.26e+00 pdb=" N PRO B 373 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.018 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" CG TYR B 495 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.80e+00 pdb=" N PRO B 479 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.027 5.00e-02 4.00e+02 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1461 2.83 - 3.35: 3742 3.35 - 3.87: 7351 3.87 - 4.38: 7584 4.38 - 4.90: 13612 Nonbonded interactions: 33750 Sorted by model distance: nonbonded pdb=" OG SER B 438 " pdb=" O PRO B 507 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR C 35 " pdb=" O ARG E 110 " model vdw 2.314 3.040 nonbonded pdb=" OD2 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.320 3.040 nonbonded pdb=" OD2 ASP E 57 " pdb=" OG SER E 104 " model vdw 2.323 3.040 nonbonded pdb=" OG SER C 203 " pdb=" OE1 GLU C 214 " model vdw 2.343 3.040 ... (remaining 33745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.140 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 0.046 4694 Z= 0.228 Angle : 0.755 8.612 6398 Z= 0.400 Chirality : 0.052 0.263 701 Planarity : 0.005 0.063 821 Dihedral : 13.383 80.311 1648 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.32), residues: 583 helix: -4.58 (0.35), residues: 18 sheet: -0.01 (0.39), residues: 163 loop : -1.50 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 353 HIS 0.005 0.002 HIS C 199 PHE 0.010 0.001 PHE B 400 TYR 0.036 0.001 TYR B 495 ARG 0.003 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.519 Fit side-chains REVERT: B 494 SER cc_start: 0.8642 (p) cc_final: 0.8441 (p) REVERT: E 31 ASP cc_start: 0.7724 (p0) cc_final: 0.7388 (p0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1352 time to fit residues: 12.8382 Evaluate side-chains 45 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 6 GLN C 39 GLN E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4694 Z= 0.223 Angle : 0.583 6.862 6398 Z= 0.306 Chirality : 0.045 0.141 701 Planarity : 0.005 0.055 821 Dihedral : 4.321 15.104 643 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.33), residues: 583 helix: -4.36 (0.49), residues: 18 sheet: -0.03 (0.35), residues: 186 loop : -1.40 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 36 HIS 0.003 0.001 HIS E 178 PHE 0.011 0.001 PHE B 374 TYR 0.018 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 494 SER cc_start: 0.8693 (p) cc_final: 0.8456 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1431 time to fit residues: 11.5998 Evaluate side-chains 43 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4694 Z= 0.162 Angle : 0.543 8.154 6398 Z= 0.277 Chirality : 0.045 0.155 701 Planarity : 0.004 0.053 821 Dihedral : 4.049 14.416 643 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.33), residues: 583 helix: -4.23 (0.56), residues: 18 sheet: -0.18 (0.35), residues: 189 loop : -1.30 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 36 HIS 0.003 0.001 HIS C 199 PHE 0.007 0.001 PHE C 33 TYR 0.025 0.001 TYR B 495 ARG 0.002 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: B 494 SER cc_start: 0.8692 (p) cc_final: 0.8444 (p) REVERT: E 154 CYS cc_start: 0.4061 (p) cc_final: 0.3644 (p) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1370 time to fit residues: 11.5146 Evaluate side-chains 43 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 39 GLN C 195 GLN E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4694 Z= 0.220 Angle : 0.578 11.429 6398 Z= 0.293 Chirality : 0.045 0.149 701 Planarity : 0.004 0.054 821 Dihedral : 4.213 15.328 643 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.33), residues: 583 helix: -3.98 (0.58), residues: 20 sheet: -0.19 (0.34), residues: 185 loop : -1.25 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 436 HIS 0.004 0.001 HIS E 214 PHE 0.010 0.002 PHE E 136 TYR 0.020 0.001 TYR B 495 ARG 0.003 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 SER cc_start: 0.8753 (p) cc_final: 0.8544 (p) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1309 time to fit residues: 10.1963 Evaluate side-chains 42 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4694 Z= 0.289 Angle : 0.641 11.829 6398 Z= 0.330 Chirality : 0.047 0.159 701 Planarity : 0.005 0.059 821 Dihedral : 4.605 15.263 643 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.33), residues: 583 helix: -3.91 (0.60), residues: 20 sheet: -0.42 (0.34), residues: 187 loop : -1.24 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 436 HIS 0.007 0.002 HIS C 199 PHE 0.012 0.002 PHE B 374 TYR 0.023 0.002 TYR B 495 ARG 0.005 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 70 MET cc_start: 0.8292 (ttm) cc_final: 0.8053 (ttm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1477 time to fit residues: 11.5269 Evaluate side-chains 47 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 39 GLN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4694 Z= 0.214 Angle : 0.595 11.903 6398 Z= 0.300 Chirality : 0.046 0.178 701 Planarity : 0.004 0.059 821 Dihedral : 4.342 15.538 643 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.33), residues: 583 helix: -3.70 (0.75), residues: 20 sheet: -0.40 (0.35), residues: 186 loop : -1.21 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 436 HIS 0.003 0.001 HIS E 214 PHE 0.008 0.001 PHE B 400 TYR 0.018 0.001 TYR B 495 ARG 0.003 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.533 Fit side-chains REVERT: E 70 MET cc_start: 0.8205 (ttm) cc_final: 0.7879 (ttm) REVERT: E 112 MET cc_start: 0.8172 (mmt) cc_final: 0.7954 (mmm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1450 time to fit residues: 11.8478 Evaluate side-chains 42 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.0050 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 0.0270 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4694 Z= 0.181 Angle : 0.587 11.284 6398 Z= 0.292 Chirality : 0.046 0.156 701 Planarity : 0.004 0.058 821 Dihedral : 4.193 15.044 643 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.34), residues: 583 helix: -3.92 (0.59), residues: 20 sheet: -0.23 (0.37), residues: 176 loop : -1.22 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.005 0.001 HIS E 178 PHE 0.007 0.001 PHE B 400 TYR 0.014 0.001 TYR B 495 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.455 Fit side-chains REVERT: B 494 SER cc_start: 0.8680 (p) cc_final: 0.8456 (p) REVERT: E 70 MET cc_start: 0.7975 (ttm) cc_final: 0.7682 (ttm) REVERT: E 112 MET cc_start: 0.8166 (mmt) cc_final: 0.7918 (mmm) REVERT: E 154 CYS cc_start: 0.4098 (p) cc_final: 0.3773 (p) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1398 time to fit residues: 11.9433 Evaluate side-chains 44 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.0770 chunk 38 optimal weight: 0.3980 chunk 28 optimal weight: 0.0570 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.0470 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 39 GLN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4694 Z= 0.143 Angle : 0.566 8.812 6398 Z= 0.282 Chirality : 0.045 0.143 701 Planarity : 0.004 0.053 821 Dihedral : 3.927 13.917 643 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.34), residues: 583 helix: -4.16 (0.49), residues: 20 sheet: -0.33 (0.35), residues: 197 loop : -1.05 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 436 HIS 0.001 0.001 HIS E 214 PHE 0.010 0.001 PHE E 136 TYR 0.030 0.001 TYR B 495 ARG 0.003 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.516 Fit side-chains REVERT: B 494 SER cc_start: 0.8587 (p) cc_final: 0.8301 (p) REVERT: C 142 THR cc_start: 0.7329 (p) cc_final: 0.7098 (p) REVERT: E 70 MET cc_start: 0.7939 (ttm) cc_final: 0.7643 (ttm) REVERT: E 112 MET cc_start: 0.8137 (mmt) cc_final: 0.7868 (mmm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1494 time to fit residues: 14.0777 Evaluate side-chains 45 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4694 Z= 0.303 Angle : 0.660 12.046 6398 Z= 0.334 Chirality : 0.047 0.160 701 Planarity : 0.005 0.055 821 Dihedral : 4.526 14.050 643 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.34), residues: 583 helix: -3.76 (0.72), residues: 20 sheet: -0.47 (0.36), residues: 187 loop : -1.12 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 436 HIS 0.006 0.002 HIS C 199 PHE 0.018 0.002 PHE B 347 TYR 0.031 0.002 TYR B 495 ARG 0.004 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: E 70 MET cc_start: 0.8038 (ttm) cc_final: 0.7736 (ttm) REVERT: E 112 MET cc_start: 0.8231 (mmt) cc_final: 0.7904 (mmm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1587 time to fit residues: 12.3756 Evaluate side-chains 43 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN E 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4694 Z= 0.177 Angle : 0.618 11.979 6398 Z= 0.307 Chirality : 0.046 0.140 701 Planarity : 0.005 0.052 821 Dihedral : 4.187 15.548 643 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.34), residues: 583 helix: -3.88 (0.64), residues: 20 sheet: -0.50 (0.35), residues: 195 loop : -1.14 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 436 HIS 0.002 0.001 HIS E 214 PHE 0.013 0.001 PHE B 347 TYR 0.025 0.001 TYR B 495 ARG 0.004 0.000 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: B 494 SER cc_start: 0.8628 (p) cc_final: 0.8365 (p) REVERT: E 46 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7756 (mp0) REVERT: E 112 MET cc_start: 0.8250 (mmt) cc_final: 0.7952 (mmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1486 time to fit residues: 13.0593 Evaluate side-chains 45 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.097726 restraints weight = 16245.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099291 restraints weight = 11221.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100377 restraints weight = 8304.238| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4694 Z= 0.184 Angle : 0.605 11.203 6398 Z= 0.301 Chirality : 0.046 0.142 701 Planarity : 0.005 0.052 821 Dihedral : 4.176 15.348 643 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.34), residues: 583 helix: -3.89 (0.64), residues: 20 sheet: -0.50 (0.35), residues: 195 loop : -1.03 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 36 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 347 TYR 0.025 0.001 TYR B 495 ARG 0.002 0.000 ARG B 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.24 seconds wall clock time: 24 minutes 1.84 seconds (1441.84 seconds total)