Starting phenix.real_space_refine on Wed Sep 25 14:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/09_2024/8fej_29029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/09_2024/8fej_29029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/09_2024/8fej_29029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/09_2024/8fej_29029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/09_2024/8fej_29029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/09_2024/8fej_29029.cif" } resolution = 4.64 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= 0.009 sd= 0.098 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 54 5.16 5 C 6606 2.51 5 N 1743 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10464 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3488 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Restraints were copied for chains: C, B Time building chain proxies: 6.61, per 1000 atoms: 0.63 Number of scatterers: 10464 At special positions: 0 Unit cell: (105.84, 111.24, 123.12, 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 54 16.00 O 2061 8.00 N 1743 7.00 C 6606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 24 sheets defined 36.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 90 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 119 through 147 removed outlier: 5.226A pdb=" N GLU A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.946A pdb=" N ASN A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.652A pdb=" N ILE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 213 removed outlier: 3.923A pdb=" N LEU A 213 " --> pdb=" O GLY A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 210 through 213' Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.585A pdb=" N LEU A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 447 through 473 removed outlier: 3.540A pdb=" N GLN A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 90 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 119 through 147 removed outlier: 5.227A pdb=" N GLU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.945A pdb=" N ASN B 175 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 209 removed outlier: 3.652A pdb=" N ILE B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 213 removed outlier: 3.922A pdb=" N LEU B 213 " --> pdb=" O GLY B 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 210 through 213' Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 234 through 242 removed outlier: 3.586A pdb=" N LEU B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 447 through 473 removed outlier: 3.541A pdb=" N GLN B 463 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 67 through 90 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 119 through 147 removed outlier: 5.226A pdb=" N GLU C 134 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.945A pdb=" N ASN C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 209 removed outlier: 3.652A pdb=" N ILE C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 213 removed outlier: 3.922A pdb=" N LEU C 213 " --> pdb=" O GLY C 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 210 through 213' Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 234 through 242 removed outlier: 3.585A pdb=" N LEU C 238 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 447 through 473 removed outlier: 3.540A pdb=" N GLN C 463 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 39 removed outlier: 6.135A pdb=" N GLU A 290 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR A 38 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 288 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.700A pdb=" N ALA A 272 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP A 263 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLU A 274 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE A 261 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.536A pdb=" N ILE A 221 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 406 removed outlier: 3.890A pdb=" N ALA A 380 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 415 through 417 removed outlier: 7.972A pdb=" N LEU A 421 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 34 through 39 removed outlier: 6.135A pdb=" N GLU B 290 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B 38 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 288 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 45 Processing sheet with id=AB3, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.700A pdb=" N ALA B 272 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP B 263 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU B 274 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 261 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 153 through 156 Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.536A pdb=" N ILE B 221 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 296 through 297 Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.891A pdb=" N ALA B 380 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 415 through 417 removed outlier: 7.916A pdb=" N LEU B 421 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 34 through 39 removed outlier: 6.134A pdb=" N GLU C 290 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR C 38 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 288 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 45 Processing sheet with id=AC2, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.701A pdb=" N ALA C 272 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP C 263 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU C 274 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE C 261 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AC4, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.536A pdb=" N ILE C 221 " --> pdb=" O GLY C 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 296 through 297 Processing sheet with id=AC6, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.890A pdb=" N ALA C 380 " --> pdb=" O SER C 405 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 3.11 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: 3486 1.35 - 1.46: 2114 1.46 - 1.58: 4927 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 10605 Sorted by residual: bond pdb=" N VAL C 181 " pdb=" CA VAL C 181 " ideal model delta sigma weight residual 1.459 1.467 -0.008 1.25e-02 6.40e+03 4.28e-01 bond pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta sigma weight residual 1.459 1.467 -0.008 1.25e-02 6.40e+03 3.68e-01 bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.459 1.466 -0.007 1.25e-02 6.40e+03 3.55e-01 bond pdb=" CG PRO A 216 " pdb=" CD PRO A 216 " ideal model delta sigma weight residual 1.503 1.485 0.018 3.40e-02 8.65e+02 2.67e-01 bond pdb=" CG PRO B 216 " pdb=" CD PRO B 216 " ideal model delta sigma weight residual 1.503 1.485 0.018 3.40e-02 8.65e+02 2.66e-01 ... (remaining 10600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 14177 1.04 - 2.08: 169 2.08 - 3.12: 48 3.12 - 4.16: 6 4.16 - 5.20: 18 Bond angle restraints: 14418 Sorted by residual: angle pdb=" C PRO B 180 " pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta sigma weight residual 121.97 126.16 -4.19 1.80e+00 3.09e-01 5.42e+00 angle pdb=" C PRO C 180 " pdb=" N VAL C 181 " pdb=" CA VAL C 181 " ideal model delta sigma weight residual 121.97 126.15 -4.18 1.80e+00 3.09e-01 5.39e+00 angle pdb=" C PRO A 180 " pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 121.97 126.15 -4.18 1.80e+00 3.09e-01 5.38e+00 angle pdb=" CA LEU C 455 " pdb=" CB LEU C 455 " pdb=" CG LEU C 455 " ideal model delta sigma weight residual 116.30 121.50 -5.20 3.50e+00 8.16e-02 2.21e+00 angle pdb=" CA LEU B 455 " pdb=" CB LEU B 455 " pdb=" CG LEU B 455 " ideal model delta sigma weight residual 116.30 121.45 -5.15 3.50e+00 8.16e-02 2.16e+00 ... (remaining 14413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 5753 16.45 - 32.90: 551 32.90 - 49.35: 155 49.35 - 65.80: 15 65.80 - 82.25: 12 Dihedral angle restraints: 6486 sinusoidal: 2508 harmonic: 3978 Sorted by residual: dihedral pdb=" CA LYS C 79 " pdb=" CB LYS C 79 " pdb=" CG LYS C 79 " pdb=" CD LYS C 79 " ideal model delta sinusoidal sigma weight residual -60.00 -116.09 56.09 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA LYS B 79 " pdb=" CB LYS B 79 " pdb=" CG LYS B 79 " pdb=" CD LYS B 79 " ideal model delta sinusoidal sigma weight residual -60.00 -116.08 56.08 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA LYS A 79 " pdb=" CB LYS A 79 " pdb=" CG LYS A 79 " pdb=" CD LYS A 79 " ideal model delta sinusoidal sigma weight residual -60.00 -116.06 56.06 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 6483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1113 0.025 - 0.050: 359 0.050 - 0.075: 136 0.075 - 0.100: 70 0.100 - 0.125: 77 Chirality restraints: 1755 Sorted by residual: chirality pdb=" CA ILE B 57 " pdb=" N ILE B 57 " pdb=" C ILE B 57 " pdb=" CB ILE B 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE B 275 " pdb=" N ILE B 275 " pdb=" C ILE B 275 " pdb=" CB ILE B 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA VAL A 444 " pdb=" N VAL A 444 " pdb=" C VAL A 444 " pdb=" CB VAL A 444 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1752 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 368 " -0.013 5.00e-02 4.00e+02 1.98e-02 6.30e-01 pdb=" N PRO C 369 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO C 369 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 369 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 368 " -0.013 5.00e-02 4.00e+02 1.97e-02 6.22e-01 pdb=" N PRO A 369 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 369 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 369 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 368 " -0.013 5.00e-02 4.00e+02 1.96e-02 6.15e-01 pdb=" N PRO B 369 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO B 369 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 369 " -0.011 5.00e-02 4.00e+02 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 99 2.60 - 3.18: 8897 3.18 - 3.75: 15888 3.75 - 4.33: 20354 4.33 - 4.90: 33529 Nonbonded interactions: 78767 Sorted by model distance: nonbonded pdb=" SG CYS B 326 " pdb=" SG CYS B 335 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 389 " pdb=" SG CYS C 412 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 389 " pdb=" SG CYS B 412 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 382 " pdb=" SG CYS B 387 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 350 " pdb=" SG CYS B 358 " model vdw 2.031 3.760 ... (remaining 78762 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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: 1.550 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.280 Find NCS groups from input model: 0.300 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 : 0.001 0.018 10605 Z= 0.078 Angle : 0.368 5.198 14418 Z= 0.189 Chirality : 0.039 0.125 1755 Planarity : 0.002 0.020 1854 Dihedral : 13.974 82.248 3915 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.86 % Favored : 96.92 % Rotamer: Outliers : 4.30 % Allowed : 14.94 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1362 helix: 2.10 (0.26), residues: 444 sheet: 0.30 (0.38), residues: 165 loop : -0.81 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 303 HIS 0.000 0.000 HIS A 130 PHE 0.002 0.000 PHE C 371 TYR 0.008 0.000 TYR C 270 ARG 0.001 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.9230 (t70) cc_final: 0.8663 (m-30) REVERT: A 157 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8298 (mm-40) REVERT: A 235 ASP cc_start: 0.8292 (m-30) cc_final: 0.8034 (p0) REVERT: A 292 MET cc_start: 0.6644 (pmm) cc_final: 0.6059 (pmm) REVERT: A 343 MET cc_start: 0.6173 (ttm) cc_final: 0.5092 (mtt) REVERT: A 347 LEU cc_start: 0.2258 (OUTLIER) cc_final: 0.1922 (tp) outliers start: 17 outliers final: 2 residues processed: 58 average time/residue: 0.1683 time to fit residues: 12.0364 Evaluate side-chains 24 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0970 chunk 102 optimal weight: 0.0870 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 105 optimal weight: 0.2980 chunk 40 optimal weight: 0.0060 chunk 64 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.1772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN C 453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10605 Z= 0.163 Angle : 0.557 7.674 14418 Z= 0.284 Chirality : 0.045 0.211 1755 Planarity : 0.004 0.055 1854 Dihedral : 3.154 17.829 1461 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.51 % Allowed : 2.53 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1362 helix: 2.22 (0.25), residues: 435 sheet: 0.26 (0.39), residues: 165 loop : -0.73 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.002 0.000 HIS B 24 PHE 0.012 0.002 PHE B 105 TYR 0.017 0.002 TYR B 74 ARG 0.026 0.001 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8996 (t70) cc_final: 0.8273 (m-30) REVERT: C 230 PHE cc_start: 0.8415 (t80) cc_final: 0.7993 (t80) REVERT: C 343 MET cc_start: 0.6064 (ttm) cc_final: 0.4301 (mtt) outliers start: 2 outliers final: 1 residues processed: 29 average time/residue: 0.1924 time to fit residues: 7.0690 Evaluate side-chains 21 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 0.0030 chunk 132 optimal weight: 0.1980 chunk 109 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10605 Z= 0.150 Angle : 0.507 8.022 14418 Z= 0.260 Chirality : 0.042 0.149 1755 Planarity : 0.004 0.056 1854 Dihedral : 3.009 11.137 1461 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1362 helix: 1.93 (0.25), residues: 435 sheet: 0.00 (0.38), residues: 165 loop : -0.85 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 303 HIS 0.004 0.001 HIS C 24 PHE 0.009 0.001 PHE C 475 TYR 0.010 0.001 TYR B 74 ARG 0.014 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9202 (t70) cc_final: 0.8588 (m-30) REVERT: B 110 MET cc_start: 0.8221 (tpt) cc_final: 0.7503 (pmm) REVERT: B 230 PHE cc_start: 0.8708 (t80) cc_final: 0.8372 (t80) REVERT: B 343 MET cc_start: 0.6024 (ttm) cc_final: 0.4037 (mtt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1378 time to fit residues: 4.1514 Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10605 Z= 0.186 Angle : 0.549 7.992 14418 Z= 0.279 Chirality : 0.043 0.127 1755 Planarity : 0.004 0.073 1854 Dihedral : 3.481 19.277 1461 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1362 helix: 1.23 (0.24), residues: 423 sheet: -0.90 (0.35), residues: 165 loop : -1.03 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 303 HIS 0.002 0.001 HIS B 253 PHE 0.011 0.002 PHE B 105 TYR 0.013 0.001 TYR C 103 ARG 0.005 0.001 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 MET cc_start: 0.8002 (tpt) cc_final: 0.7692 (pmm) REVERT: B 230 PHE cc_start: 0.8919 (t80) cc_final: 0.8551 (t80) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1292 time to fit residues: 3.9263 Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.0010 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 111 optimal weight: 0.0770 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.0770 chunk 117 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10605 Z= 0.111 Angle : 0.465 6.676 14418 Z= 0.232 Chirality : 0.041 0.131 1755 Planarity : 0.003 0.054 1854 Dihedral : 3.151 12.962 1461 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1362 helix: 1.32 (0.24), residues: 432 sheet: -0.76 (0.35), residues: 165 loop : -1.26 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 303 HIS 0.001 0.000 HIS C 130 PHE 0.009 0.001 PHE C 105 TYR 0.006 0.001 TYR B 249 ARG 0.002 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: B 230 PHE cc_start: 0.8950 (t80) cc_final: 0.8573 (t80) REVERT: B 343 MET cc_start: 0.6232 (ttm) cc_final: 0.4418 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1316 time to fit residues: 4.1612 Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 0.3980 chunk 25 optimal weight: 0.0000 chunk 76 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 108 optimal weight: 0.0010 chunk 60 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 0.0170 overall best weight: 0.0566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10605 Z= 0.120 Angle : 0.489 6.413 14418 Z= 0.245 Chirality : 0.042 0.155 1755 Planarity : 0.003 0.038 1854 Dihedral : 3.132 12.056 1461 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.51 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1362 helix: 1.27 (0.24), residues: 432 sheet: -0.71 (0.35), residues: 165 loop : -1.39 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 303 HIS 0.000 0.000 HIS C 253 PHE 0.007 0.001 PHE B 105 TYR 0.005 0.001 TYR A 202 ARG 0.001 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 230 PHE cc_start: 0.8970 (t80) cc_final: 0.8571 (t80) REVERT: B 343 MET cc_start: 0.6115 (ttm) cc_final: 0.4290 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1296 time to fit residues: 4.1562 Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 0.0670 chunk 60 optimal weight: 0.0370 chunk 80 optimal weight: 0.0870 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10605 Z= 0.104 Angle : 0.480 8.445 14418 Z= 0.230 Chirality : 0.041 0.147 1755 Planarity : 0.003 0.035 1854 Dihedral : 3.004 11.409 1461 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1362 helix: 1.33 (0.24), residues: 420 sheet: -0.68 (0.35), residues: 165 loop : -1.34 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS C 253 PHE 0.006 0.001 PHE C 475 TYR 0.005 0.001 TYR C 202 ARG 0.001 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 230 PHE cc_start: 0.9027 (t80) cc_final: 0.8590 (t80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1736 time to fit residues: 5.4548 Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.0020 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 0.0870 chunk 102 optimal weight: 0.0870 chunk 118 optimal weight: 0.0980 chunk 124 optimal weight: 0.8980 overall best weight: 0.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10605 Z= 0.110 Angle : 0.473 7.524 14418 Z= 0.231 Chirality : 0.041 0.140 1755 Planarity : 0.004 0.066 1854 Dihedral : 2.996 10.894 1461 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.95 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1362 helix: 1.09 (0.24), residues: 438 sheet: -0.69 (0.35), residues: 165 loop : -1.43 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS A 253 PHE 0.006 0.001 PHE A 475 TYR 0.006 0.001 TYR B 202 ARG 0.010 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: B 129 LEU cc_start: 0.8301 (tp) cc_final: 0.8030 (pp) REVERT: B 230 PHE cc_start: 0.9013 (t80) cc_final: 0.8620 (t80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2207 time to fit residues: 6.8059 Evaluate side-chains 17 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0970 chunk 121 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 72 optimal weight: 0.0870 chunk 52 optimal weight: 0.0270 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 109 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10605 Z= 0.112 Angle : 0.475 7.036 14418 Z= 0.232 Chirality : 0.041 0.138 1755 Planarity : 0.003 0.045 1854 Dihedral : 2.947 10.966 1461 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1362 helix: 1.18 (0.24), residues: 426 sheet: -0.69 (0.36), residues: 165 loop : -1.32 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.001 0.000 HIS C 130 PHE 0.006 0.001 PHE A 475 TYR 0.005 0.001 TYR C 202 ARG 0.007 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 230 PHE cc_start: 0.9054 (t80) cc_final: 0.8718 (t80) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1217 time to fit residues: 3.9300 Evaluate side-chains 17 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10605 Z= 0.109 Angle : 0.473 6.916 14418 Z= 0.232 Chirality : 0.041 0.135 1755 Planarity : 0.003 0.046 1854 Dihedral : 2.962 12.204 1461 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.05 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1362 helix: 1.30 (0.25), residues: 426 sheet: -0.71 (0.35), residues: 165 loop : -1.27 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 303 HIS 0.000 0.000 HIS A 24 PHE 0.009 0.001 PHE C 230 TYR 0.005 0.001 TYR B 367 ARG 0.005 0.000 ARG A 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: B 230 PHE cc_start: 0.9104 (t80) cc_final: 0.8802 (t80) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1003 time to fit residues: 3.2718 Evaluate side-chains 17 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 98 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 0.0050 chunk 107 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.0010 chunk 94 optimal weight: 0.0070 overall best weight: 0.1176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.052279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.042414 restraints weight = 59907.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.042916 restraints weight = 51112.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.043203 restraints weight = 45329.125| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10605 Z= 0.106 Angle : 0.475 7.013 14418 Z= 0.232 Chirality : 0.041 0.137 1755 Planarity : 0.003 0.038 1854 Dihedral : 2.910 11.162 1461 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.17 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1362 helix: 1.22 (0.24), residues: 426 sheet: -0.77 (0.36), residues: 162 loop : -1.26 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 303 HIS 0.000 0.000 HIS A 253 PHE 0.006 0.001 PHE C 230 TYR 0.006 0.001 TYR C 202 ARG 0.005 0.000 ARG B 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1654.17 seconds wall clock time: 30 minutes 34.92 seconds (1834.92 seconds total)