Starting phenix.real_space_refine on Thu Dec 7 23:36:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/12_2023/8gv3_34282_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/12_2023/8gv3_34282.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/12_2023/8gv3_34282_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/12_2023/8gv3_34282_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/12_2023/8gv3_34282_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/12_2023/8gv3_34282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/12_2023/8gv3_34282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/12_2023/8gv3_34282_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/12_2023/8gv3_34282_updated.pdb" } resolution = 3.05 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= -0.002 sd= 0.238 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4 5.49 5 S 46 5.16 5 C 3634 2.51 5 N 954 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 222": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5720 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} Conformer: "B" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} bond proxies already assigned to first conformer: 2822 Chain: "B" Number of atoms: 2778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} Conformer: "B" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} bond proxies already assigned to first conformer: 2822 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' ZN': 2, 'NAD': 1, 'WKZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' ZN': 2, 'NAD': 1, 'WKZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 696 SG CYS A 96 83.998 27.246 17.420 1.00 53.43 S ATOM 715 SG CYS A 99 80.541 26.704 19.076 1.00 59.54 S ATOM 741 SG CYS A 102 81.036 29.728 17.005 1.00 49.33 S ATOM 802 SG CYS A 110 82.922 29.536 20.183 1.00 47.97 S ATOM 323 SG CYS A 44 83.107 47.740 31.478 1.00 59.70 S ATOM 1275 SG CYS A 173 81.944 45.551 28.014 1.00 47.81 S ATOM 3474 SG CYS B 96 36.999 47.553 17.420 1.00 53.45 S ATOM 3493 SG CYS B 99 40.458 48.095 19.072 1.00 60.78 S ATOM 3519 SG CYS B 102 39.962 45.071 17.004 1.00 50.91 S ATOM 3580 SG CYS B 110 38.078 45.265 20.184 1.00 48.57 S ATOM 3101 SG CYS B 44 37.894 27.060 31.479 1.00 60.48 S ATOM 4053 SG CYS B 173 39.057 29.247 28.014 1.00 47.65 S Time building chain proxies: 6.28, per 1000 atoms: 1.10 Number of scatterers: 5720 At special positions: 0 Unit cell: (122.1, 75.9, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 46 16.00 P 4 15.00 O 1078 8.00 N 954 7.00 C 3634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.02 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 110 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 102 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 99 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 96 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 173 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 44 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS A 66 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 102 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 99 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 96 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 173 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 44 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS B 66 " Number of angles added : 12 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 10 sheets defined 28.2% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.665A pdb=" N LYS A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 201 through 213 Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.359A pdb=" N ALA A 229 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 249 through 257 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 323 through 335 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.762A pdb=" N PHE A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.666A pdb=" N LYS B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 201 through 213 Processing helix chain 'B' and resid 225 through 234 removed outlier: 4.357A pdb=" N ALA B 229 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 249 through 257 Processing helix chain 'B' and resid 271 through 280 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 323 through 335 Proline residue: B 328 - end of helix Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.766A pdb=" N PHE B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 11 Processing sheet with id= B, first strand: chain 'A' and resid 148 through 152 removed outlier: 3.802A pdb=" N SER A 74 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS A 37 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 72 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 40 through 43 removed outlier: 4.868A pdb=" N THR A 369 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 370 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN A 348 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS A 372 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER A 350 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 129 through 131 removed outlier: 4.292A pdb=" N PHE A 129 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.250A pdb=" N SER A 288 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 217 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL A 196 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 219 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU A 238 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 5 through 11 Processing sheet with id= G, first strand: chain 'B' and resid 148 through 152 removed outlier: 3.799A pdb=" N SER B 74 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS B 37 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 72 " --> pdb=" O LYS B 37 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 40 through 43 removed outlier: 4.874A pdb=" N THR B 369 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL B 370 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN B 348 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS B 372 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER B 350 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 129 through 131 removed outlier: 4.291A pdb=" N PHE B 129 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 313 through 315 removed outlier: 6.249A pdb=" N SER B 288 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 217 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL B 196 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 219 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B 238 " --> pdb=" O GLY B 220 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 958 1.31 - 1.43: 1399 1.43 - 1.56: 3393 1.56 - 1.68: 28 1.68 - 1.81: 58 Bond restraints: 5836 Sorted by residual: bond pdb=" C3B NAD A 403 " pdb=" C4B NAD A 403 " ideal model delta sigma weight residual 1.523 1.253 0.270 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C3B NAD B 403 " pdb=" C4B NAD B 403 " ideal model delta sigma weight residual 1.523 1.253 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C1B NAD B 403 " pdb=" C2B NAD B 403 " ideal model delta sigma weight residual 1.534 1.272 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C1B NAD A 403 " pdb=" C2B NAD A 403 " ideal model delta sigma weight residual 1.534 1.272 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAD A 403 " pdb=" C2D NAD A 403 " ideal model delta sigma weight residual 1.528 1.269 0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 5831 not shown) Histogram of bond angle deviations from ideal: 97.99 - 106.94: 191 106.94 - 115.90: 3768 115.90 - 124.86: 3850 124.86 - 133.82: 99 133.82 - 142.77: 10 Bond angle restraints: 7918 Sorted by residual: angle pdb=" C1B NAD B 403 " pdb=" N9A NAD B 403 " pdb=" C4A NAD B 403 " ideal model delta sigma weight residual 126.46 108.58 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C1B NAD A 403 " pdb=" N9A NAD A 403 " pdb=" C4A NAD A 403 " ideal model delta sigma weight residual 126.46 108.60 17.86 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C1B NAD B 403 " pdb=" N9A NAD B 403 " pdb=" C8A NAD B 403 " ideal model delta sigma weight residual 127.40 142.77 -15.37 3.00e+00 1.11e-01 2.63e+01 angle pdb=" C1B NAD A 403 " pdb=" N9A NAD A 403 " pdb=" C8A NAD A 403 " ideal model delta sigma weight residual 127.40 142.71 -15.31 3.00e+00 1.11e-01 2.60e+01 angle pdb=" O1A NAD A 403 " pdb=" PA NAD A 403 " pdb=" O2A NAD A 403 " ideal model delta sigma weight residual 122.64 109.21 13.43 3.00e+00 1.11e-01 2.00e+01 ... (remaining 7913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 3076 15.55 - 31.10: 335 31.10 - 46.65: 65 46.65 - 62.20: 40 62.20 - 77.75: 8 Dihedral angle restraints: 3524 sinusoidal: 1426 harmonic: 2098 Sorted by residual: dihedral pdb=" CA LYS A 322 " pdb=" C LYS A 322 " pdb=" N SER A 323 " pdb=" CA SER A 323 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LYS B 322 " pdb=" C LYS B 322 " pdb=" N SER B 323 " pdb=" CA SER B 323 " ideal model delta harmonic sigma weight residual -180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA THR A 312 " pdb=" C THR A 312 " pdb=" N TRP A 313 " pdb=" CA TRP A 313 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 3521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 697 0.060 - 0.119: 187 0.119 - 0.179: 20 0.179 - 0.239: 2 0.239 - 0.298: 2 Chirality restraints: 908 Sorted by residual: chirality pdb=" C3D NAD A 403 " pdb=" C2D NAD A 403 " pdb=" C4D NAD A 403 " pdb=" O3D NAD A 403 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3D NAD B 403 " pdb=" C2D NAD B 403 " pdb=" C4D NAD B 403 " pdb=" O3D NAD B 403 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3B NAD A 403 " pdb=" C2B NAD A 403 " pdb=" C4B NAD A 403 " pdb=" O3B NAD A 403 " both_signs ideal model delta sigma weight residual False -2.71 -2.48 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 905 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 313 " -0.003 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP B 313 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 313 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP B 313 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 313 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP B 313 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 313 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 313 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 313 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 313 " 0.003 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP A 313 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 313 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 313 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 313 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP A 313 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 313 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 313 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 313 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 373 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C ILE A 373 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE A 373 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 374 " 0.010 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 643 2.75 - 3.28: 5210 3.28 - 3.82: 8583 3.82 - 4.36: 10911 4.36 - 4.90: 19161 Nonbonded interactions: 44508 Sorted by model distance: nonbonded pdb=" OD2 ASP B 124 " pdb=" NH2 ARG B 128 " model vdw 2.208 2.520 nonbonded pdb=" OD2 ASP A 124 " pdb=" NH2 ARG A 128 " model vdw 2.209 2.520 nonbonded pdb=" O CYS A 173 " pdb=" OG1 THR A 177 " model vdw 2.223 2.440 nonbonded pdb=" O CYS B 173 " pdb=" OG1 THR B 177 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP B 222 " pdb=" N ILE B 223 " model vdw 2.265 2.520 ... (remaining 44503 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' and (resid 2 through 335 or resid 337 through 374 or resid 401 throug \ h 404)) selection = (chain 'B' and (resid 2 through 335 or resid 337 through 374 or resid 401 throug \ h 404)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.620 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 24.530 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.015 0.270 5836 Z= 1.012 Angle : 0.974 17.881 7918 Z= 0.429 Chirality : 0.055 0.298 908 Planarity : 0.005 0.044 992 Dihedral : 14.998 77.754 2188 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.29), residues: 744 helix: -0.80 (0.33), residues: 220 sheet: 0.35 (0.44), residues: 140 loop : -1.05 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP A 313 HIS 0.004 0.001 HIS A 138 PHE 0.017 0.002 PHE B 351 TYR 0.014 0.002 TYR A 179 ARG 0.003 0.001 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.647 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1831 time to fit residues: 20.0794 Evaluate side-chains 68 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.650 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5836 Z= 0.245 Angle : 0.546 5.769 7918 Z= 0.279 Chirality : 0.046 0.133 908 Planarity : 0.004 0.038 992 Dihedral : 9.530 54.430 906 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.00 % Allowed : 4.65 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.77 (0.29), residues: 744 helix: -0.32 (0.34), residues: 224 sheet: 0.56 (0.45), residues: 140 loop : -1.01 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 313 HIS 0.002 0.001 HIS B 138 PHE 0.005 0.001 PHE A 351 TYR 0.011 0.001 TYR A 179 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.656 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.1916 time to fit residues: 18.8103 Evaluate side-chains 70 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0680 time to fit residues: 1.2112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5836 Z= 0.259 Angle : 0.536 5.800 7918 Z= 0.273 Chirality : 0.046 0.131 908 Planarity : 0.004 0.038 992 Dihedral : 9.342 57.456 906 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.00 % Allowed : 5.81 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.67 (0.30), residues: 744 helix: -0.17 (0.34), residues: 224 sheet: 0.54 (0.45), residues: 140 loop : -0.95 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 313 HIS 0.002 0.001 HIS A 138 PHE 0.006 0.001 PHE B 351 TYR 0.010 0.001 TYR B 92 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.647 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.2021 time to fit residues: 19.2987 Evaluate side-chains 70 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0866 time to fit residues: 1.3817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5836 Z= 0.277 Angle : 0.542 5.899 7918 Z= 0.276 Chirality : 0.046 0.132 908 Planarity : 0.004 0.037 992 Dihedral : 9.270 59.535 906 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.66 % Allowed : 6.31 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.67 (0.30), residues: 744 helix: -0.14 (0.35), residues: 224 sheet: 0.52 (0.45), residues: 140 loop : -0.97 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 313 HIS 0.003 0.001 HIS A 138 PHE 0.005 0.001 PHE A 351 TYR 0.010 0.001 TYR B 92 ARG 0.001 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.613 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 69 average time/residue: 0.1796 time to fit residues: 16.6814 Evaluate side-chains 72 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0594 time to fit residues: 1.9116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5836 Z= 0.350 Angle : 0.572 6.383 7918 Z= 0.292 Chirality : 0.047 0.137 908 Planarity : 0.004 0.038 992 Dihedral : 9.281 58.018 906 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.33 % Allowed : 7.64 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.76 (0.30), residues: 744 helix: -0.18 (0.34), residues: 222 sheet: 0.45 (0.46), residues: 140 loop : -1.04 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 313 HIS 0.003 0.001 HIS A 138 PHE 0.006 0.001 PHE B 197 TYR 0.011 0.002 TYR A 92 ARG 0.001 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.658 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.1930 time to fit residues: 18.1657 Evaluate side-chains 68 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.608 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0910 time to fit residues: 1.1122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 5836 Z= 0.398 Angle : 0.605 6.688 7918 Z= 0.310 Chirality : 0.049 0.140 908 Planarity : 0.005 0.040 992 Dihedral : 9.305 56.808 906 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.00 % Allowed : 10.13 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.88 (0.29), residues: 744 helix: -0.25 (0.34), residues: 222 sheet: 0.41 (0.46), residues: 140 loop : -1.14 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 313 HIS 0.003 0.001 HIS A 138 PHE 0.007 0.002 PHE B 197 TYR 0.012 0.002 TYR A 92 ARG 0.001 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.637 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1992 time to fit residues: 17.7468 Evaluate side-chains 72 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0660 time to fit residues: 1.3174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.0980 chunk 8 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5836 Z= 0.116 Angle : 0.461 5.291 7918 Z= 0.232 Chirality : 0.044 0.121 908 Planarity : 0.004 0.036 992 Dihedral : 8.989 56.330 906 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.33 % Allowed : 10.30 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.30), residues: 744 helix: 0.14 (0.36), residues: 226 sheet: 0.61 (0.45), residues: 140 loop : -0.94 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 313 HIS 0.001 0.000 HIS A 138 PHE 0.005 0.001 PHE B 318 TYR 0.007 0.001 TYR A 92 ARG 0.001 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.644 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 73 average time/residue: 0.1772 time to fit residues: 17.4551 Evaluate side-chains 66 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0934 time to fit residues: 1.1577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5836 Z= 0.306 Angle : 0.550 6.199 7918 Z= 0.280 Chirality : 0.047 0.134 908 Planarity : 0.004 0.036 992 Dihedral : 9.095 57.033 906 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.66 % Allowed : 11.96 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.65 (0.30), residues: 744 helix: -0.08 (0.35), residues: 224 sheet: 0.52 (0.46), residues: 140 loop : -0.97 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 313 HIS 0.003 0.001 HIS A 138 PHE 0.005 0.001 PHE A 197 TYR 0.011 0.001 TYR B 92 ARG 0.001 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.649 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 69 average time/residue: 0.1988 time to fit residues: 17.9999 Evaluate side-chains 69 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0563 time to fit residues: 1.2738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5836 Z= 0.166 Angle : 0.481 5.537 7918 Z= 0.243 Chirality : 0.044 0.123 908 Planarity : 0.004 0.034 992 Dihedral : 8.945 57.132 906 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.17 % Allowed : 11.79 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.52 (0.31), residues: 744 helix: 0.08 (0.36), residues: 226 sheet: 0.46 (0.46), residues: 142 loop : -0.89 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 321 HIS 0.002 0.001 HIS A 138 PHE 0.004 0.001 PHE A 318 TYR 0.008 0.001 TYR B 92 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.746 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 67 average time/residue: 0.1902 time to fit residues: 16.9044 Evaluate side-chains 65 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0593 time to fit residues: 0.9987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5836 Z= 0.292 Angle : 0.543 6.143 7918 Z= 0.275 Chirality : 0.047 0.134 908 Planarity : 0.004 0.035 992 Dihedral : 9.020 57.745 906 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.30), residues: 744 helix: -0.01 (0.35), residues: 224 sheet: 0.49 (0.46), residues: 140 loop : -0.96 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 313 HIS 0.003 0.001 HIS B 138 PHE 0.005 0.001 PHE A 197 TYR 0.015 0.002 TYR B 179 ARG 0.001 0.000 ARG A 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.664 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1958 time to fit residues: 16.7566 Evaluate side-chains 65 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 0.0170 chunk 60 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.144556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109108 restraints weight = 17004.603| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.00 r_work: 0.2957 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5836 Z= 0.130 Angle : 0.463 5.286 7918 Z= 0.232 Chirality : 0.044 0.120 908 Planarity : 0.004 0.033 992 Dihedral : 8.842 58.059 906 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.17 % Allowed : 12.62 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.31), residues: 744 helix: 0.17 (0.36), residues: 226 sheet: 0.50 (0.46), residues: 142 loop : -0.86 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 321 HIS 0.002 0.001 HIS B 138 PHE 0.004 0.001 PHE A 318 TYR 0.007 0.001 TYR A 92 ARG 0.001 0.000 ARG A 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1401.86 seconds wall clock time: 26 minutes 9.34 seconds (1569.34 seconds total)