Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:54:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9f_32366/11_2022/7w9f_32366.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9f_32366/11_2022/7w9f_32366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9f_32366/11_2022/7w9f_32366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9f_32366/11_2022/7w9f_32366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9f_32366/11_2022/7w9f_32366.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w9f_32366/11_2022/7w9f_32366.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 405": "OD1" <-> "OD2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 427": "OD1" <-> "OD2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E GLU 484": "OE1" <-> "OE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4856 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1671 Classifications: {'peptide': 220} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 202} Chain: "B" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1643 Classifications: {'peptide': 211} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Time building chain proxies: 3.24, per 1000 atoms: 0.67 Number of scatterers: 4856 At special positions: 0 Unit cell: (63.394, 92.905, 137.718, 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 22 16.00 O 961 8.00 N 807 7.00 C 3066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 609.1 milliseconds 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 7.7% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 4.070A pdb=" N LYS A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.627A pdb=" N ASP A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.627A pdb=" N TYR A 104 " --> pdb=" O TYR A 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.796A pdb=" N LEU B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'E' and resid 337 through 343 removed outlier: 4.003A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.733A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.759A pdb=" N VAL A 18 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 22 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 79 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.558A pdb=" N GLU A 10 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 117 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER A 40 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 45 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 50 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 59 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.657A pdb=" N VAL A 143 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 188 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 147 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 186 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 184 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR A 182 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.657A pdb=" N VAL A 143 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 188 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 147 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 186 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 184 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR A 182 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 161 removed outlier: 3.663A pdb=" N THR A 211 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.675A pdb=" N PHE B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 72 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.729A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.841A pdb=" N ASN B 137 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.792A pdb=" N ASN B 145 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 149 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 193 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.966A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA E 397 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'E' and resid 473 through 474 125 hydrogen bonds defined for protein. 303 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: 1.33 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1538 1.34 - 1.46: 1249 1.46 - 1.58: 2167 1.58 - 1.70: 0 1.70 - 1.81: 28 Bond restraints: 4982 Sorted by residual: bond pdb=" CA PRO A 133 " pdb=" C PRO A 133 " ideal model delta sigma weight residual 1.516 1.539 -0.023 1.42e-02 4.96e+03 2.55e+00 bond pdb=" N THR B 51 " pdb=" CA THR B 51 " ideal model delta sigma weight residual 1.462 1.484 -0.022 1.48e-02 4.57e+03 2.22e+00 bond pdb=" C PRO A 133 " pdb=" N GLY A 134 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.40e-02 5.10e+03 2.07e+00 bond pdb=" C TYR A 101 " pdb=" N PRO A 102 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.45e+00 bond pdb=" CB LYS E 458 " pdb=" CG LYS E 458 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 ... (remaining 4977 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.55: 154 106.55 - 113.40: 2604 113.40 - 120.25: 1731 120.25 - 127.10: 2236 127.10 - 133.95: 60 Bond angle restraints: 6785 Sorted by residual: angle pdb=" C SER B 50 " pdb=" N THR B 51 " pdb=" CA THR B 51 " ideal model delta sigma weight residual 122.61 129.74 -7.13 1.56e+00 4.11e-01 2.09e+01 angle pdb=" CA PRO A 133 " pdb=" C PRO A 133 " pdb=" N GLY A 134 " ideal model delta sigma weight residual 117.98 123.82 -5.84 1.43e+00 4.89e-01 1.67e+01 angle pdb=" N PRO A 133 " pdb=" CA PRO A 133 " pdb=" C PRO A 133 " ideal model delta sigma weight residual 113.40 118.54 -5.14 1.34e+00 5.57e-01 1.47e+01 angle pdb=" C PRO A 133 " pdb=" N GLY A 134 " pdb=" CA GLY A 134 " ideal model delta sigma weight residual 123.00 132.38 -9.38 3.00e+00 1.11e-01 9.77e+00 angle pdb=" C GLY A 100 " pdb=" N TYR A 101 " pdb=" CA TYR A 101 " ideal model delta sigma weight residual 120.09 123.38 -3.29 1.25e+00 6.40e-01 6.95e+00 ... (remaining 6780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2672 17.92 - 35.83: 239 35.83 - 53.75: 36 53.75 - 71.66: 8 71.66 - 89.58: 4 Dihedral angle restraints: 2959 sinusoidal: 1136 harmonic: 1823 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 143.74 -50.74 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 140.42 -47.42 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA TYR A 105 " pdb=" C TYR A 105 " pdb=" N ALA A 106 " pdb=" CA ALA A 106 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 585 0.058 - 0.116: 133 0.116 - 0.174: 19 0.174 - 0.232: 3 0.232 - 0.289: 2 Chirality restraints: 742 Sorted by residual: chirality pdb=" CB ILE E 468 " pdb=" CA ILE E 468 " pdb=" CG1 ILE E 468 " pdb=" CG2 ILE E 468 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA PRO A 133 " pdb=" N PRO A 133 " pdb=" C PRO A 133 " pdb=" CB PRO A 133 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 739 not shown) Planarity restraints: 874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 155 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 156 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 101 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 102 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 462 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO E 463 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " -0.026 5.00e-02 4.00e+02 ... (remaining 871 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1574 2.82 - 3.34: 3720 3.34 - 3.86: 7775 3.86 - 4.38: 8405 4.38 - 4.90: 14864 Nonbonded interactions: 36338 Sorted by model distance: nonbonded pdb=" OD1 ASP B 82 " pdb=" OH TYR B 86 " model vdw 2.302 2.440 nonbonded pdb=" O SER A 179 " pdb=" OG SER A 179 " model vdw 2.322 2.440 nonbonded pdb=" O ILE B 150 " pdb=" OG SER B 153 " model vdw 2.325 2.440 nonbonded pdb=" O SER B 171 " pdb=" OG SER B 171 " model vdw 2.330 2.440 nonbonded pdb=" OH TYR B 36 " pdb=" OE1 GLN B 89 " model vdw 2.354 2.440 ... (remaining 36333 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3066 2.51 5 N 807 2.21 5 O 961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.340 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: 0.010 Extract box with map and model: 1.610 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 17.030 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 0.034 4982 Z= 0.226 Angle : 0.725 9.379 6785 Z= 0.389 Chirality : 0.051 0.289 742 Planarity : 0.006 0.048 874 Dihedral : 13.990 89.579 1775 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.28), residues: 619 helix: -5.15 (0.17), residues: 28 sheet: -1.84 (0.29), residues: 249 loop : -2.69 (0.26), residues: 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1572 time to fit residues: 27.6555 Evaluate side-chains 130 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.0010 chunk 46 optimal weight: 0.0020 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 56 optimal weight: 1.9990 overall best weight: 0.1810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 140 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 124 GLN B 138 ASN B 166 GLN B 190 ASN E 460 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4982 Z= 0.135 Angle : 0.538 12.869 6785 Z= 0.274 Chirality : 0.042 0.154 742 Planarity : 0.005 0.049 874 Dihedral : 4.166 20.897 685 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.29), residues: 619 helix: -4.81 (0.21), residues: 33 sheet: -1.16 (0.30), residues: 253 loop : -2.20 (0.29), residues: 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 0.482 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 143 average time/residue: 0.1391 time to fit residues: 26.2097 Evaluate side-chains 146 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0470 time to fit residues: 1.2311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 38 optimal weight: 0.0770 chunk 15 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 0.0030 chunk 45 optimal weight: 0.7980 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4982 Z= 0.134 Angle : 0.520 12.561 6785 Z= 0.261 Chirality : 0.042 0.175 742 Planarity : 0.004 0.049 874 Dihedral : 3.938 19.823 685 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.31), residues: 619 helix: -4.17 (0.43), residues: 33 sheet: -0.81 (0.32), residues: 245 loop : -1.66 (0.31), residues: 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 0.552 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 150 average time/residue: 0.1505 time to fit residues: 29.3976 Evaluate side-chains 149 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 0.583 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0478 time to fit residues: 1.0582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 4982 Z= 0.247 Angle : 0.568 12.460 6785 Z= 0.287 Chirality : 0.043 0.155 742 Planarity : 0.004 0.051 874 Dihedral : 4.276 28.704 685 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.32), residues: 619 helix: -3.61 (0.59), residues: 33 sheet: -0.81 (0.31), residues: 256 loop : -1.58 (0.32), residues: 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.543 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 141 average time/residue: 0.1334 time to fit residues: 24.7542 Evaluate side-chains 139 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0497 time to fit residues: 1.3822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.0470 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4982 Z= 0.156 Angle : 0.528 12.410 6785 Z= 0.265 Chirality : 0.042 0.147 742 Planarity : 0.004 0.051 874 Dihedral : 4.017 23.787 685 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.73 (0.33), residues: 619 helix: -3.23 (0.68), residues: 33 sheet: -0.63 (0.33), residues: 247 loop : -1.28 (0.33), residues: 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.563 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 139 average time/residue: 0.1388 time to fit residues: 25.5533 Evaluate side-chains 138 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0456 time to fit residues: 1.1607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.0060 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4982 Z= 0.151 Angle : 0.520 12.599 6785 Z= 0.262 Chirality : 0.042 0.150 742 Planarity : 0.004 0.053 874 Dihedral : 3.974 21.863 685 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.50 (0.33), residues: 619 helix: -3.08 (0.72), residues: 33 sheet: -0.52 (0.33), residues: 247 loop : -1.09 (0.34), residues: 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.556 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 144 average time/residue: 0.1349 time to fit residues: 25.7829 Evaluate side-chains 141 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0471 time to fit residues: 1.1996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 4982 Z= 0.284 Angle : 0.583 12.599 6785 Z= 0.297 Chirality : 0.044 0.174 742 Planarity : 0.004 0.052 874 Dihedral : 4.414 29.884 685 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: 619 helix: -3.02 (0.70), residues: 33 sheet: -0.26 (0.34), residues: 241 loop : -1.28 (0.33), residues: 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 0.520 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 138 average time/residue: 0.1457 time to fit residues: 26.3241 Evaluate side-chains 134 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0491 time to fit residues: 0.8818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4982 Z= 0.136 Angle : 0.535 12.423 6785 Z= 0.271 Chirality : 0.043 0.154 742 Planarity : 0.004 0.054 874 Dihedral : 4.030 19.065 685 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.15 (0.35), residues: 619 helix: -2.86 (0.77), residues: 33 sheet: -0.26 (0.34), residues: 243 loop : -0.87 (0.35), residues: 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.643 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 134 average time/residue: 0.1485 time to fit residues: 26.2511 Evaluate side-chains 134 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0497 time to fit residues: 1.1386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4982 Z= 0.201 Angle : 0.569 12.363 6785 Z= 0.288 Chirality : 0.044 0.190 742 Planarity : 0.004 0.051 874 Dihedral : 4.141 22.981 685 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.14 (0.35), residues: 619 helix: -2.87 (0.76), residues: 33 sheet: -0.19 (0.34), residues: 255 loop : -0.93 (0.35), residues: 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.557 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1377 time to fit residues: 24.3536 Evaluate side-chains 133 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4982 Z= 0.188 Angle : 0.582 12.434 6785 Z= 0.294 Chirality : 0.044 0.191 742 Planarity : 0.004 0.053 874 Dihedral : 4.202 21.487 685 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.11 (0.34), residues: 619 helix: -2.86 (0.75), residues: 33 sheet: -0.13 (0.34), residues: 249 loop : -0.93 (0.35), residues: 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.544 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 0.1489 time to fit residues: 24.8336 Evaluate side-chains 127 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0488 time to fit residues: 0.9470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.133149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.120893 restraints weight = 7760.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124730 restraints weight = 3895.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127208 restraints weight = 2243.859| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4982 Z= 0.199 Angle : 0.580 12.350 6785 Z= 0.295 Chirality : 0.044 0.187 742 Planarity : 0.004 0.052 874 Dihedral : 4.233 21.480 685 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.71 % Cis-general : 0.51 % 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: -1.10 (0.34), residues: 619 helix: -2.81 (0.78), residues: 33 sheet: -0.14 (0.34), residues: 249 loop : -0.91 (0.35), residues: 337 =============================================================================== Job complete usr+sys time: 1367.96 seconds wall clock time: 26 minutes 7.37 seconds (1567.37 seconds total)