Starting phenix.real_space_refine on Fri Mar 15 03:20:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/03_2024/8fej_29029.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/03_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_29029/03_2024/8fej_29029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/03_2024/8fej_29029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/03_2024/8fej_29029.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/03_2024/8fej_29029.pdb" } 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 Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10464 Number of models: 1 Model: "" Number of chains: 3 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} Chain: "B" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3488 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain: "C" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3488 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Time building chain proxies: 6.15, per 1000 atoms: 0.59 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=15, 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 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 2.2 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: 1.37 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: 3.10 Time building geometry restraints manager: 4.10 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: 100.84 - 107.46: 237 107.46 - 114.08: 6304 114.08 - 120.69: 4091 120.69 - 127.31: 3741 127.31 - 133.93: 45 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: 5769 16.45 - 32.90: 561 32.90 - 49.35: 159 49.35 - 65.80: 15 65.80 - 82.25: 12 Dihedral angle restraints: 6516 sinusoidal: 2538 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 6513 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: 2.25 - 2.78: 2244 2.78 - 3.31: 9986 3.31 - 3.84: 16675 3.84 - 4.37: 18175 4.37 - 4.90: 31657 Nonbonded interactions: 78737 Sorted by model distance: nonbonded pdb=" NZ LYS A 50 " pdb=" O MET A 241 " model vdw 2.253 2.520 nonbonded pdb=" NZ LYS B 50 " pdb=" O MET B 241 " model vdw 2.253 2.520 nonbonded pdb=" NZ LYS C 50 " pdb=" O MET C 241 " model vdw 2.253 2.520 nonbonded pdb=" ND2 ASN B 233 " pdb=" OE2 GLU B 236 " model vdw 2.288 2.520 nonbonded pdb=" ND2 ASN A 233 " pdb=" OE2 GLU A 236 " model vdw 2.289 2.520 ... (remaining 78732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.880 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: 4.020 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.250 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.690 ------------------------------------------------------------------------------- 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= 0.079 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 : 2.253 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 : 0.357 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: 0.1526 time to fit residues: 10.9989 Evaluate side-chains 24 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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: 0.7980 chunk 102 optimal weight: 0.0670 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 20.0000 chunk 105 optimal weight: 0.0870 chunk 40 optimal weight: 0.0370 chunk 64 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 10605 Z= 0.158 Angle : 0.541 7.688 14418 Z= 0.274 Chirality : 0.044 0.229 1755 Planarity : 0.003 0.036 1854 Dihedral : 3.039 16.482 1461 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.51 % Allowed : 2.03 % Favored : 97.47 % 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: 0.61 (0.24), residues: 1362 helix: 2.28 (0.25), residues: 444 sheet: 0.29 (0.39), residues: 165 loop : -0.75 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.000 HIS B 24 PHE 0.013 0.002 PHE B 105 TYR 0.017 0.001 TYR B 74 ARG 0.029 0.001 ARG A 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 : 0.399 Fit side-chains revert: symmetry clash REVERT: C 52 MET cc_start: 0.4477 (tpp) cc_final: 0.4236 (tpp) REVERT: C 72 ASP cc_start: 0.9011 (t70) cc_final: 0.8278 (m-30) REVERT: C 230 PHE cc_start: 0.8340 (t80) cc_final: 0.7850 (t80) REVERT: C 343 MET cc_start: 0.6073 (ttm) cc_final: 0.4335 (mtt) outliers start: 2 outliers final: 1 residues processed: 29 average time/residue: 0.1580 time to fit residues: 6.1324 Evaluate side-chains 20 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 0.8980 chunk 38 optimal weight: 0.3980 chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 132 optimal weight: 0.0470 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 98 optimal weight: 0.0770 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 398 GLN ** 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: 0.6936 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 10605 Z= 0.139 Angle : 0.480 6.757 14418 Z= 0.241 Chirality : 0.042 0.164 1755 Planarity : 0.003 0.040 1854 Dihedral : 2.926 11.392 1461 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 0.35 (0.23), residues: 1362 helix: 2.13 (0.25), residues: 441 sheet: 0.09 (0.39), residues: 165 loop : -0.93 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.001 0.000 HIS A 24 PHE 0.009 0.001 PHE C 105 TYR 0.010 0.001 TYR B 74 ARG 0.021 0.001 ARG C 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 23 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9130 (t70) cc_final: 0.8530 (m-30) REVERT: B 230 PHE cc_start: 0.8597 (t80) cc_final: 0.8276 (t80) REVERT: B 343 MET cc_start: 0.5789 (ttm) cc_final: 0.3701 (mtt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1353 time to fit residues: 4.4638 Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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: 6.9990 chunk 92 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 116 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 224 GLN B 289 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10605 Z= 0.114 Angle : 0.462 7.832 14418 Z= 0.228 Chirality : 0.041 0.130 1755 Planarity : 0.005 0.119 1854 Dihedral : 2.925 13.715 1461 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.63 % Favored : 95.15 % 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: -0.16 (0.22), residues: 1362 helix: 1.47 (0.24), residues: 435 sheet: -0.23 (0.37), residues: 165 loop : -1.04 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.000 HIS B 24 PHE 0.026 0.002 PHE C 277 TYR 0.008 0.001 TYR B 74 ARG 0.001 0.000 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 22 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9159 (t70) cc_final: 0.8556 (m-30) REVERT: B 92 MET cc_start: 0.6534 (tpp) cc_final: 0.6329 (tpt) REVERT: B 230 PHE cc_start: 0.8840 (t80) cc_final: 0.8474 (t80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1259 time to fit residues: 3.9631 Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 4.9990 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.4980 chunk 117 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 398 GLN ** 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: 0.7023 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10605 Z= 0.132 Angle : 0.502 6.664 14418 Z= 0.250 Chirality : 0.041 0.152 1755 Planarity : 0.004 0.073 1854 Dihedral : 3.095 17.764 1461 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.95 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: -0.33 (0.22), residues: 1362 helix: 1.55 (0.24), residues: 441 sheet: -0.57 (0.36), residues: 165 loop : -1.26 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS B 253 PHE 0.039 0.002 PHE B 277 TYR 0.005 0.001 TYR B 74 ARG 0.001 0.000 ARG B 171 *********************** 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 : 0.400 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9215 (t70) cc_final: 0.8687 (m-30) REVERT: B 230 PHE cc_start: 0.8936 (t80) cc_final: 0.8515 (t80) REVERT: B 241 MET cc_start: 0.2765 (ptm) cc_final: 0.2067 (mtm) REVERT: B 343 MET cc_start: 0.5700 (ttm) cc_final: 0.3776 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1268 time to fit residues: 4.0377 Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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: 0.9980 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 10 optimal weight: 9.9990 chunk 68 optimal weight: 0.0000 chunk 125 optimal weight: 7.9990 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7007 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10605 Z= 0.106 Angle : 0.454 6.973 14418 Z= 0.221 Chirality : 0.041 0.140 1755 Planarity : 0.003 0.038 1854 Dihedral : 2.919 12.834 1461 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % 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: -0.40 (0.22), residues: 1362 helix: 1.54 (0.24), residues: 438 sheet: -0.57 (0.36), residues: 165 loop : -1.35 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.001 0.000 HIS B 253 PHE 0.009 0.002 PHE A 277 TYR 0.006 0.001 TYR C 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 : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9190 (t70) cc_final: 0.8594 (m-30) REVERT: B 230 PHE cc_start: 0.8964 (t80) cc_final: 0.8529 (t80) REVERT: B 241 MET cc_start: 0.2738 (ptm) cc_final: 0.2141 (ptt) REVERT: B 343 MET cc_start: 0.5740 (ttm) cc_final: 0.3821 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1109 time to fit residues: 3.5019 Evaluate side-chains 19 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 1.9990 chunk 74 optimal weight: 0.0000 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 0.0370 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 0.0570 chunk 130 optimal weight: 0.0030 chunk 81 optimal weight: 0.0170 chunk 79 optimal weight: 0.0000 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 224 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10605 Z= 0.106 Angle : 0.469 7.903 14418 Z= 0.224 Chirality : 0.041 0.164 1755 Planarity : 0.003 0.029 1854 Dihedral : 2.928 12.670 1461 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.17 % Favored : 93.61 % 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: -0.60 (0.22), residues: 1362 helix: 1.31 (0.24), residues: 441 sheet: -0.62 (0.36), residues: 165 loop : -1.45 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS C 130 PHE 0.006 0.001 PHE C 475 TYR 0.006 0.001 TYR B 202 ARG 0.001 0.000 ARG C 325 *********************** 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 : 0.441 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9161 (t70) cc_final: 0.8565 (m-30) REVERT: B 230 PHE cc_start: 0.8996 (t80) cc_final: 0.8564 (t80) REVERT: B 241 MET cc_start: 0.2598 (ptm) cc_final: 0.2055 (ptt) REVERT: B 343 MET cc_start: 0.5410 (ttm) cc_final: 0.3388 (mtt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1610 time to fit residues: 4.9135 Evaluate side-chains 19 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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: 0.9980 chunk 77 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 82 optimal weight: 0.0040 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 124 optimal weight: 0.0030 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7000 moved from start: 0.3556 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= 0.115 Angle : 0.477 7.114 14418 Z= 0.234 Chirality : 0.041 0.159 1755 Planarity : 0.004 0.064 1854 Dihedral : 2.909 11.882 1461 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.17 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.59 (0.22), residues: 1362 helix: 1.42 (0.24), residues: 438 sheet: -0.58 (0.36), residues: 165 loop : -1.51 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 303 HIS 0.000 0.000 HIS B 130 PHE 0.006 0.001 PHE A 475 TYR 0.007 0.001 TYR B 202 ARG 0.012 0.001 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 : 0.393 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9191 (t70) cc_final: 0.8600 (m-30) REVERT: B 230 PHE cc_start: 0.9057 (t80) cc_final: 0.8639 (t80) REVERT: B 241 MET cc_start: 0.2679 (ptm) cc_final: 0.2467 (ptm) REVERT: B 343 MET cc_start: 0.5484 (ttm) cc_final: 0.3409 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1301 time to fit residues: 4.1456 Evaluate side-chains 19 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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: 0.8980 chunk 121 optimal weight: 0.0970 chunk 124 optimal weight: 0.0060 chunk 72 optimal weight: 0.0770 chunk 52 optimal weight: 0.0070 chunk 95 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 109 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 79 optimal weight: 0.0060 overall best weight: 0.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6969 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10605 Z= 0.113 Angle : 0.474 7.155 14418 Z= 0.230 Chirality : 0.041 0.155 1755 Planarity : 0.003 0.050 1854 Dihedral : 2.906 11.885 1461 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.17 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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 (0.21), residues: 1362 helix: 1.19 (0.24), residues: 438 sheet: -0.48 (0.37), residues: 162 loop : -1.42 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.001 0.000 HIS C 130 PHE 0.006 0.001 PHE B 475 TYR 0.006 0.001 TYR B 202 ARG 0.006 0.000 ARG A 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 23 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9129 (t70) cc_final: 0.8527 (m-30) REVERT: B 110 MET cc_start: 0.7111 (tpt) cc_final: 0.6851 (pmm) REVERT: B 230 PHE cc_start: 0.9042 (t80) cc_final: 0.8635 (t80) REVERT: B 343 MET cc_start: 0.5417 (ttm) cc_final: 0.3263 (mtt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1345 time to fit residues: 4.4569 Evaluate side-chains 19 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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: 0.0370 chunk 78 optimal weight: 30.0000 chunk 60 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 0.0570 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 398 GLN ** 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: 0.6993 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10605 Z= 0.113 Angle : 0.476 6.901 14418 Z= 0.232 Chirality : 0.041 0.153 1755 Planarity : 0.003 0.051 1854 Dihedral : 2.890 11.271 1461 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.61 (0.22), residues: 1362 helix: 1.28 (0.24), residues: 438 sheet: -0.50 (0.36), residues: 162 loop : -1.45 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS C 130 PHE 0.016 0.002 PHE C 277 TYR 0.005 0.001 TYR B 202 ARG 0.006 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 22 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9169 (t70) cc_final: 0.8568 (m-30) REVERT: B 110 MET cc_start: 0.7387 (tpt) cc_final: 0.6859 (pmm) REVERT: B 230 PHE cc_start: 0.9106 (t80) cc_final: 0.8727 (t80) REVERT: B 241 MET cc_start: 0.2549 (ptt) cc_final: 0.2274 (ptt) REVERT: B 343 MET cc_start: 0.5502 (ttm) cc_final: 0.3467 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1318 time to fit residues: 4.2603 Evaluate side-chains 20 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 107 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 224 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.053241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.043179 restraints weight = 59981.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.043736 restraints weight = 50996.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.044123 restraints weight = 44887.047| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3983 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= 0.113 Angle : 0.470 6.937 14418 Z= 0.229 Chirality : 0.041 0.149 1755 Planarity : 0.003 0.056 1854 Dihedral : 2.872 10.662 1461 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.51 % Favored : 94.27 % 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: -0.55 (0.22), residues: 1362 helix: 1.43 (0.24), residues: 426 sheet: -0.62 (0.35), residues: 165 loop : -1.41 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.000 0.000 HIS B 253 PHE 0.010 0.001 PHE A 277 TYR 0.016 0.001 TYR B 202 ARG 0.006 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1651.86 seconds wall clock time: 30 minutes 47.53 seconds (1847.53 seconds total)