Starting phenix.real_space_refine on Sat Feb 17 13:57:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/02_2024/8b14_15802_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/02_2024/8b14_15802.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/02_2024/8b14_15802_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/02_2024/8b14_15802_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/02_2024/8b14_15802_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/02_2024/8b14_15802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/02_2024/8b14_15802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/02_2024/8b14_15802_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/02_2024/8b14_15802_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14 atoms to isotropic. 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 P 2 5.49 5 S 36 5.16 5 C 6114 2.51 5 N 1631 2.21 5 O 1915 1.98 5 H 9112 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 40": "OD1" <-> "OD2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 466": "OD1" <-> "OD2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 506": "OD1" <-> "OD2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 616": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18810 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 10595 Classifications: {'peptide': 696} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 662} Chain breaks: 1 Chain: "B" Number of atoms: 8065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 8065 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 25, 'TRANS': 521} Chain breaks: 3 Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'DDQ': 1, 'LU9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.64, per 1000 atoms: 0.46 Number of scatterers: 18810 At special positions: 0 Unit cell: (102.044, 108.356, 137.812, 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) S 36 16.00 P 2 15.00 O 1915 8.00 N 1631 7.00 C 6114 6.00 H 9112 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 701 " - pdb=" SG CYS A 707 " 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: 15.58 Conformation dependent library (CDL) restraints added in 2.0 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 15 sheets defined 6.7% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 21 through 27 removed outlier: 3.530A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 137 through 140 No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 327 through 330 No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.866A pdb=" N ARG B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP B 153 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 507 through 510 Processing helix chain 'B' and resid 519 through 522 Processing sheet with id= A, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.734A pdb=" N VAL A 152 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A 129 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN A 150 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 131 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 148 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 174 through 181 removed outlier: 4.186A pdb=" N LYS A 162 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A 573 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 574 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR A 555 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 576 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR A 553 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY A 578 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASN A 551 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLU A 580 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 549 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU A 582 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLY A 547 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS A 584 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL A 545 " --> pdb=" O LYS A 584 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP A 487 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 509 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N PHE A 485 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 345 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 218 through 221 Processing sheet with id= D, first strand: chain 'A' and resid 434 through 439 Processing sheet with id= E, first strand: chain 'A' and resid 698 through 701 removed outlier: 7.097A pdb=" N PHE A 708 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 63 through 66 Processing sheet with id= G, first strand: chain 'B' and resid 94 through 96 Processing sheet with id= H, first strand: chain 'B' and resid 254 through 258 removed outlier: 6.625A pdb=" N TYR B 601 " --> pdb=" O PHE B 559 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR B 561 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 599 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS B 563 " --> pdb=" O TYR B 597 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR B 597 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR B 565 " --> pdb=" O GLY B 595 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY B 595 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL B 567 " --> pdb=" O GLN B 593 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN B 593 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 615 " --> pdb=" O HIS B 481 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N HIS B 481 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER B 617 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SER B 479 " --> pdb=" O SER B 617 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 229 through 231 Processing sheet with id= J, first strand: chain 'B' and resid 245 through 247 Processing sheet with id= K, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= L, first strand: chain 'B' and resid 358 through 360 removed outlier: 3.577A pdb=" N ASN B 380 " --> pdb=" O ASN B 420 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 422 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY B 378 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 424 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP B 376 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 398 through 401 Processing sheet with id= N, first strand: chain 'B' and resid 464 through 468 Processing sheet with id= O, first strand: chain 'B' and resid 471 through 474 409 hydrogen bonds defined for protein. 1128 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: 8.43 Time building geometry restraints manager: 15.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9105 1.03 - 1.23: 69 1.23 - 1.42: 4263 1.42 - 1.62: 5539 1.62 - 1.81: 65 Bond restraints: 19041 Sorted by residual: bond pdb=" C81 LU9 A 802 " pdb=" O81 LU9 A 802 " ideal model delta sigma weight residual 1.185 1.395 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C71 LU9 A 802 " pdb=" O71 LU9 A 802 " ideal model delta sigma weight residual 1.181 1.372 -0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" C01 LU9 A 802 " pdb=" O03 LU9 A 802 " ideal model delta sigma weight residual 1.261 1.414 -0.153 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C01 LU9 A 802 " pdb=" O02 LU9 A 802 " ideal model delta sigma weight residual 1.257 1.402 -0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C2 LU9 A 802 " pdb=" O05 LU9 A 802 " ideal model delta sigma weight residual 1.362 1.495 -0.133 2.00e-02 2.50e+03 4.44e+01 ... (remaining 19036 not shown) Histogram of bond angle deviations from ideal: 99.65 - 107.01: 1576 107.01 - 114.37: 21030 114.37 - 121.73: 7666 121.73 - 129.09: 3756 129.09 - 136.45: 53 Bond angle restraints: 34081 Sorted by residual: angle pdb=" C19 LU9 A 802 " pdb="C110 LU9 A 802 " pdb="C111 LU9 A 802 " ideal model delta sigma weight residual 109.52 136.45 -26.93 3.00e+00 1.11e-01 8.06e+01 angle pdb=" N GLY B 191 " pdb=" CA GLY B 191 " pdb=" C GLY B 191 " ideal model delta sigma weight residual 113.27 118.94 -5.67 1.33e+00 5.65e-01 1.82e+01 angle pdb=" C02 LU9 A 802 " pdb=" C01 LU9 A 802 " pdb=" O02 LU9 A 802 " ideal model delta sigma weight residual 119.95 108.01 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C72 LU9 A 802 " pdb=" C71 LU9 A 802 " pdb=" O71 LU9 A 802 " ideal model delta sigma weight residual 119.98 108.96 11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C02 LU9 A 802 " pdb=" C01 LU9 A 802 " pdb=" O03 LU9 A 802 " ideal model delta sigma weight residual 119.93 109.14 10.79 3.00e+00 1.11e-01 1.29e+01 ... (remaining 34076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 8757 34.98 - 69.95: 360 69.95 - 104.93: 34 104.93 - 139.90: 4 139.90 - 174.88: 1 Dihedral angle restraints: 9156 sinusoidal: 4916 harmonic: 4240 Sorted by residual: dihedral pdb=" C58 LU9 A 802 " pdb=" C59 LU9 A 802 " pdb="C510 LU9 A 802 " pdb="C511 LU9 A 802 " ideal model delta sinusoidal sigma weight residual 201.93 27.05 174.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C18 LU9 A 802 " pdb=" C19 LU9 A 802 " pdb="C110 LU9 A 802 " pdb="C111 LU9 A 802 " ideal model delta sinusoidal sigma weight residual 184.62 65.66 118.96 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C85 LU9 A 802 " pdb=" C86 LU9 A 802 " pdb=" C87 LU9 A 802 " pdb=" C88 LU9 A 802 " ideal model delta sinusoidal sigma weight residual -178.03 -63.83 -114.20 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 9153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1150 0.051 - 0.101: 210 0.101 - 0.152: 75 0.152 - 0.202: 1 0.202 - 0.253: 2 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C2 LU9 A 802 " pdb=" C3 LU9 A 802 " pdb=" O05 LU9 A 802 " pdb=" O6 LU9 A 802 " both_signs ideal model delta sigma weight residual False -2.34 -2.60 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ASN B 609 " pdb=" N ASN B 609 " pdb=" C ASN B 609 " pdb=" CB ASN B 609 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB2 LU9 A 802 " pdb=" CB1 LU9 A 802 " pdb=" NB2 LU9 A 802 " pdb=" CB3 LU9 A 802 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 1435 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C81 LU9 A 802 " 0.362 2.00e-02 2.50e+03 2.09e-01 4.36e+02 pdb=" C82 LU9 A 802 " -0.112 2.00e-02 2.50e+03 pdb=" O73 LU9 A 802 " -0.124 2.00e-02 2.50e+03 pdb=" O81 LU9 A 802 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" OB3 LU9 A 802 " -0.124 2.00e-02 2.50e+03 2.08e-01 4.32e+02 pdb=" C71 LU9 A 802 " 0.360 2.00e-02 2.50e+03 pdb=" C72 LU9 A 802 " -0.108 2.00e-02 2.50e+03 pdb=" O71 LU9 A 802 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 LU9 A 802 " -0.351 2.00e-02 2.50e+03 2.02e-01 4.10e+02 pdb=" C02 LU9 A 802 " 0.108 2.00e-02 2.50e+03 pdb=" O02 LU9 A 802 " 0.121 2.00e-02 2.50e+03 pdb=" O03 LU9 A 802 " 0.122 2.00e-02 2.50e+03 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 593 2.08 - 2.71: 31588 2.71 - 3.34: 53803 3.34 - 3.97: 77061 3.97 - 4.60: 117926 Nonbonded interactions: 280971 Sorted by model distance: nonbonded pdb=" O PRO B 237 " pdb=" HG SER B 269 " model vdw 1.456 1.850 nonbonded pdb="HH11 ARG A 384 " pdb=" O07 LU9 A 802 " model vdw 1.457 1.850 nonbonded pdb=" HH TYR A 87 " pdb=" HH TYR A 275 " model vdw 1.466 2.100 nonbonded pdb=" HZ2 LYS B 383 " pdb=" O SER B 385 " model vdw 1.469 1.850 nonbonded pdb=" O GLY B 198 " pdb=" HH TYR B 268 " model vdw 1.492 1.850 ... (remaining 280966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 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: 6.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.290 Extract box with map and model: 18.350 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 66.520 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.007 0.210 9929 Z= 0.463 Angle : 0.683 26.925 13476 Z= 0.328 Chirality : 0.046 0.253 1438 Planarity : 0.009 0.209 1761 Dihedral : 17.163 174.880 3584 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.79 % Allowed : 14.17 % Favored : 85.04 % 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: 0.27 (0.24), residues: 1231 helix: -2.15 (0.58), residues: 69 sheet: 0.86 (0.24), residues: 540 loop : -0.07 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 187 HIS 0.004 0.001 HIS B 546 PHE 0.011 0.001 PHE B 89 TYR 0.025 0.002 TYR B 192 ARG 0.003 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 216 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7978 (ttmm) REVERT: A 127 GLU cc_start: 0.7478 (tp30) cc_final: 0.7196 (tp30) REVERT: A 308 SER cc_start: 0.8581 (t) cc_final: 0.8370 (p) REVERT: A 353 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7598 (mp-120) REVERT: A 379 ASP cc_start: 0.7789 (t0) cc_final: 0.7568 (t70) REVERT: A 510 GLU cc_start: 0.7481 (tt0) cc_final: 0.7262 (tt0) REVERT: A 534 VAL cc_start: 0.8920 (t) cc_final: 0.8674 (p) REVERT: A 556 ASN cc_start: 0.8564 (t0) cc_final: 0.8335 (t0) REVERT: A 592 ASN cc_start: 0.8437 (m110) cc_final: 0.8183 (m110) REVERT: A 668 ASP cc_start: 0.7892 (m-30) cc_final: 0.7691 (m-30) REVERT: B 41 SER cc_start: 0.7618 (m) cc_final: 0.7161 (p) REVERT: B 73 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7398 (tm-30) REVERT: B 134 LEU cc_start: 0.8451 (mt) cc_final: 0.8221 (mt) REVERT: B 385 SER cc_start: 0.8237 (t) cc_final: 0.7926 (p) REVERT: B 610 ASN cc_start: 0.7658 (m-40) cc_final: 0.7324 (m110) outliers start: 8 outliers final: 3 residues processed: 221 average time/residue: 2.4405 time to fit residues: 581.8150 Evaluate side-chains 193 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain B residue 112 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 354 ASN A 436 ASN A 592 ASN A 714 GLN B 115 GLN B 321 ASN B 360 ASN B 475 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 9929 Z= 0.551 Angle : 0.637 5.684 13476 Z= 0.333 Chirality : 0.050 0.153 1438 Planarity : 0.005 0.050 1761 Dihedral : 10.922 109.919 1468 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.76 % Allowed : 15.55 % Favored : 81.69 % 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: 0.01 (0.24), residues: 1231 helix: -2.45 (0.54), residues: 70 sheet: 0.73 (0.23), residues: 526 loop : -0.25 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 187 HIS 0.006 0.001 HIS B 546 PHE 0.017 0.002 PHE A 365 TYR 0.018 0.002 TYR B 597 ARG 0.009 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7732 (mp0) cc_final: 0.7417 (mp0) REVERT: A 64 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7980 (ttmm) REVERT: A 127 GLU cc_start: 0.7464 (tp30) cc_final: 0.7242 (tp30) REVERT: A 199 ARG cc_start: 0.8188 (ttt-90) cc_final: 0.7925 (ttp80) REVERT: A 478 ASP cc_start: 0.7505 (m-30) cc_final: 0.7200 (m-30) REVERT: A 510 GLU cc_start: 0.7536 (tt0) cc_final: 0.7325 (tt0) REVERT: A 534 VAL cc_start: 0.8890 (t) cc_final: 0.8607 (p) REVERT: A 556 ASN cc_start: 0.8504 (t0) cc_final: 0.8300 (t0) REVERT: B 41 SER cc_start: 0.7593 (m) cc_final: 0.7181 (p) REVERT: B 73 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 299 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8894 (mp) REVERT: B 359 ILE cc_start: 0.8460 (mt) cc_final: 0.8240 (mm) REVERT: B 360 ASN cc_start: 0.8016 (t0) cc_final: 0.7728 (t0) REVERT: B 385 SER cc_start: 0.8386 (t) cc_final: 0.8108 (p) REVERT: B 610 ASN cc_start: 0.7550 (m-40) cc_final: 0.7276 (m-40) outliers start: 28 outliers final: 17 residues processed: 212 average time/residue: 2.4069 time to fit residues: 550.8801 Evaluate side-chains 212 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 0.0970 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 38 optimal weight: 0.0670 chunk 89 optimal weight: 0.0770 overall best weight: 0.0872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 238 ASN B 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9929 Z= 0.146 Angle : 0.500 4.886 13476 Z= 0.261 Chirality : 0.046 0.153 1438 Planarity : 0.004 0.059 1761 Dihedral : 9.277 104.027 1461 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.38 % Allowed : 16.34 % Favored : 82.28 % 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: 0.12 (0.24), residues: 1231 helix: -1.90 (0.62), residues: 70 sheet: 0.66 (0.23), residues: 523 loop : -0.09 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 187 HIS 0.003 0.001 HIS B 546 PHE 0.008 0.001 PHE A 365 TYR 0.009 0.001 TYR B 109 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7727 (mp0) cc_final: 0.7445 (mp0) REVERT: A 127 GLU cc_start: 0.7464 (tp30) cc_final: 0.7235 (tp30) REVERT: A 159 GLU cc_start: 0.7355 (mp0) cc_final: 0.7045 (pm20) REVERT: A 225 ASP cc_start: 0.7364 (p0) cc_final: 0.7133 (p0) REVERT: A 308 SER cc_start: 0.8529 (m) cc_final: 0.8253 (p) REVERT: A 478 ASP cc_start: 0.7486 (m-30) cc_final: 0.7213 (m-30) REVERT: A 510 GLU cc_start: 0.7508 (tt0) cc_final: 0.7300 (tt0) REVERT: A 534 VAL cc_start: 0.8898 (t) cc_final: 0.8586 (p) REVERT: A 556 ASN cc_start: 0.8489 (t0) cc_final: 0.8273 (t0) REVERT: B 41 SER cc_start: 0.7550 (m) cc_final: 0.7129 (p) REVERT: B 54 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8108 (ptm160) REVERT: B 73 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7355 (tm-30) REVERT: B 359 ILE cc_start: 0.8458 (mt) cc_final: 0.8231 (mm) REVERT: B 360 ASN cc_start: 0.8088 (t0) cc_final: 0.7737 (t0) REVERT: B 385 SER cc_start: 0.8405 (t) cc_final: 0.8120 (p) REVERT: B 610 ASN cc_start: 0.7545 (m-40) cc_final: 0.7266 (m-40) outliers start: 14 outliers final: 9 residues processed: 201 average time/residue: 2.5213 time to fit residues: 545.3655 Evaluate side-chains 205 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 547 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 0.0370 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN A 690 ASN B 238 ASN B 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 9929 Z= 0.532 Angle : 0.597 5.279 13476 Z= 0.310 Chirality : 0.049 0.151 1438 Planarity : 0.004 0.066 1761 Dihedral : 8.967 104.915 1461 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.66 % Allowed : 15.94 % Favored : 81.40 % 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: -0.08 (0.24), residues: 1231 helix: -2.20 (0.58), residues: 71 sheet: 0.48 (0.22), residues: 535 loop : -0.16 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 187 HIS 0.007 0.002 HIS A 339 PHE 0.015 0.002 PHE A 365 TYR 0.017 0.002 TYR B 597 ARG 0.004 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7777 (mp0) cc_final: 0.7470 (mp0) REVERT: A 127 GLU cc_start: 0.7448 (tp30) cc_final: 0.7231 (tp30) REVERT: A 225 ASP cc_start: 0.7366 (p0) cc_final: 0.7102 (p0) REVERT: A 478 ASP cc_start: 0.7498 (m-30) cc_final: 0.7223 (m-30) REVERT: A 534 VAL cc_start: 0.8872 (t) cc_final: 0.8575 (p) REVERT: A 556 ASN cc_start: 0.8529 (t0) cc_final: 0.8326 (t0) REVERT: B 41 SER cc_start: 0.7649 (m) cc_final: 0.7222 (p) REVERT: B 54 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8140 (ptm160) REVERT: B 73 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 134 LEU cc_start: 0.8481 (mt) cc_final: 0.8279 (mt) REVERT: B 359 ILE cc_start: 0.8454 (mt) cc_final: 0.8213 (mm) REVERT: B 610 ASN cc_start: 0.7546 (m-40) cc_final: 0.7274 (m-40) REVERT: B 619 MET cc_start: 0.8809 (mtt) cc_final: 0.8558 (mtp) REVERT: B 633 LYS cc_start: 0.8472 (tttm) cc_final: 0.8237 (tttm) outliers start: 27 outliers final: 18 residues processed: 211 average time/residue: 2.5753 time to fit residues: 585.2667 Evaluate side-chains 216 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 547 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9929 Z= 0.487 Angle : 0.596 5.595 13476 Z= 0.309 Chirality : 0.048 0.152 1438 Planarity : 0.004 0.067 1761 Dihedral : 8.608 98.590 1461 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.95 % Allowed : 15.85 % Favored : 81.20 % 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: -0.25 (0.24), residues: 1231 helix: -2.35 (0.56), residues: 71 sheet: 0.32 (0.22), residues: 537 loop : -0.23 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 187 HIS 0.007 0.001 HIS B 546 PHE 0.013 0.002 PHE A 365 TYR 0.017 0.002 TYR B 597 ARG 0.004 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7796 (mp0) cc_final: 0.7481 (mp0) REVERT: A 127 GLU cc_start: 0.7445 (tp30) cc_final: 0.7223 (tp30) REVERT: A 159 GLU cc_start: 0.7250 (mp0) cc_final: 0.6896 (pm20) REVERT: A 225 ASP cc_start: 0.7367 (p0) cc_final: 0.7045 (p0) REVERT: A 238 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7868 (mt-10) REVERT: A 478 ASP cc_start: 0.7497 (m-30) cc_final: 0.7239 (m-30) REVERT: A 534 VAL cc_start: 0.8865 (t) cc_final: 0.8568 (p) REVERT: B 41 SER cc_start: 0.7621 (m) cc_final: 0.7190 (p) REVERT: B 54 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8115 (ptm160) REVERT: B 73 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 359 ILE cc_start: 0.8462 (mt) cc_final: 0.8225 (mm) REVERT: B 385 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 610 ASN cc_start: 0.7558 (m-40) cc_final: 0.7308 (m-40) outliers start: 30 outliers final: 19 residues processed: 218 average time/residue: 2.5257 time to fit residues: 592.1273 Evaluate side-chains 223 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 114 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9929 Z= 0.363 Angle : 0.554 5.331 13476 Z= 0.287 Chirality : 0.046 0.148 1438 Planarity : 0.004 0.067 1761 Dihedral : 8.393 101.630 1461 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.26 % Allowed : 17.22 % Favored : 80.51 % 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: -0.22 (0.24), residues: 1231 helix: -2.15 (0.59), residues: 71 sheet: 0.29 (0.22), residues: 536 loop : -0.18 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 187 HIS 0.004 0.001 HIS B 546 PHE 0.012 0.001 PHE A 365 TYR 0.014 0.001 TYR B 597 ARG 0.002 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7791 (mp0) cc_final: 0.7480 (mp0) REVERT: A 127 GLU cc_start: 0.7440 (tp30) cc_final: 0.7227 (tp30) REVERT: A 225 ASP cc_start: 0.7369 (p0) cc_final: 0.7133 (p0) REVERT: A 228 ASN cc_start: 0.8611 (t0) cc_final: 0.8395 (t0) REVERT: A 238 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 478 ASP cc_start: 0.7578 (m-30) cc_final: 0.7307 (m-30) REVERT: A 534 VAL cc_start: 0.8868 (t) cc_final: 0.8567 (p) REVERT: B 41 SER cc_start: 0.7623 (m) cc_final: 0.7193 (p) REVERT: B 73 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7353 (tm-30) REVERT: B 359 ILE cc_start: 0.8440 (mt) cc_final: 0.8196 (mm) REVERT: B 610 ASN cc_start: 0.7567 (m-40) cc_final: 0.7284 (m-40) outliers start: 23 outliers final: 19 residues processed: 214 average time/residue: 2.5527 time to fit residues: 587.2727 Evaluate side-chains 224 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 205 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.0070 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 475 GLN B 631 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9929 Z= 0.346 Angle : 0.545 5.252 13476 Z= 0.282 Chirality : 0.046 0.146 1438 Planarity : 0.004 0.067 1761 Dihedral : 8.187 99.187 1461 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.46 % Allowed : 17.13 % Favored : 80.41 % 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: -0.21 (0.24), residues: 1231 helix: -2.04 (0.60), residues: 71 sheet: 0.28 (0.22), residues: 536 loop : -0.16 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 187 HIS 0.004 0.001 HIS B 546 PHE 0.011 0.001 PHE A 365 TYR 0.013 0.001 TYR B 597 ARG 0.002 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 209 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7791 (mp0) cc_final: 0.7483 (mp0) REVERT: A 127 GLU cc_start: 0.7434 (tp30) cc_final: 0.7220 (tp30) REVERT: A 159 GLU cc_start: 0.7227 (mp0) cc_final: 0.6920 (pm20) REVERT: A 225 ASP cc_start: 0.7374 (p0) cc_final: 0.7130 (p0) REVERT: A 228 ASN cc_start: 0.8600 (t0) cc_final: 0.8388 (t0) REVERT: A 478 ASP cc_start: 0.7560 (m-30) cc_final: 0.7289 (m-30) REVERT: A 534 VAL cc_start: 0.8868 (t) cc_final: 0.8567 (p) REVERT: B 41 SER cc_start: 0.7619 (m) cc_final: 0.7192 (p) REVERT: B 73 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7325 (tm-30) REVERT: B 359 ILE cc_start: 0.8439 (mt) cc_final: 0.8190 (mm) REVERT: B 610 ASN cc_start: 0.7574 (m-40) cc_final: 0.7305 (m-40) outliers start: 25 outliers final: 20 residues processed: 221 average time/residue: 2.4884 time to fit residues: 592.3517 Evaluate side-chains 223 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.0370 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9929 Z= 0.347 Angle : 0.543 5.833 13476 Z= 0.281 Chirality : 0.046 0.144 1438 Planarity : 0.004 0.067 1761 Dihedral : 8.023 98.653 1461 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.07 % Allowed : 17.81 % Favored : 80.12 % 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: -0.19 (0.24), residues: 1231 helix: -1.97 (0.61), residues: 71 sheet: 0.29 (0.22), residues: 536 loop : -0.15 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 187 HIS 0.004 0.001 HIS A 339 PHE 0.011 0.001 PHE A 365 TYR 0.013 0.001 TYR B 597 ARG 0.002 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 209 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7789 (mp0) cc_final: 0.7481 (mp0) REVERT: A 127 GLU cc_start: 0.7429 (tp30) cc_final: 0.7217 (tp30) REVERT: A 159 GLU cc_start: 0.7222 (mp0) cc_final: 0.6929 (pm20) REVERT: A 225 ASP cc_start: 0.7375 (p0) cc_final: 0.7130 (p0) REVERT: A 228 ASN cc_start: 0.8601 (t0) cc_final: 0.8382 (t0) REVERT: A 478 ASP cc_start: 0.7573 (m-30) cc_final: 0.7308 (m-30) REVERT: A 534 VAL cc_start: 0.8854 (t) cc_final: 0.8556 (p) REVERT: B 41 SER cc_start: 0.7617 (m) cc_final: 0.7190 (p) REVERT: B 54 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7523 (ptt90) REVERT: B 73 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7313 (tm-30) REVERT: B 359 ILE cc_start: 0.8446 (mt) cc_final: 0.8198 (mm) REVERT: B 385 SER cc_start: 0.8514 (t) cc_final: 0.8238 (p) REVERT: B 610 ASN cc_start: 0.7694 (m-40) cc_final: 0.7411 (m-40) outliers start: 21 outliers final: 18 residues processed: 219 average time/residue: 2.4599 time to fit residues: 582.0505 Evaluate side-chains 223 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 72 optimal weight: 0.0970 chunk 116 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9929 Z= 0.341 Angle : 0.542 5.380 13476 Z= 0.280 Chirality : 0.046 0.147 1438 Planarity : 0.004 0.067 1761 Dihedral : 7.894 97.607 1461 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.87 % Allowed : 18.11 % Favored : 80.02 % 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: -0.18 (0.24), residues: 1231 helix: -1.91 (0.62), residues: 71 sheet: 0.28 (0.22), residues: 536 loop : -0.14 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 187 HIS 0.004 0.001 HIS A 339 PHE 0.011 0.001 PHE A 365 TYR 0.014 0.001 TYR B 597 ARG 0.003 0.000 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7786 (mp0) cc_final: 0.7481 (mp0) REVERT: A 159 GLU cc_start: 0.7227 (mp0) cc_final: 0.7000 (pm20) REVERT: A 225 ASP cc_start: 0.7347 (p0) cc_final: 0.7084 (p0) REVERT: A 228 ASN cc_start: 0.8603 (t0) cc_final: 0.8382 (t0) REVERT: A 478 ASP cc_start: 0.7563 (m-30) cc_final: 0.7289 (m-30) REVERT: A 534 VAL cc_start: 0.8852 (t) cc_final: 0.8556 (p) REVERT: B 41 SER cc_start: 0.7621 (m) cc_final: 0.7188 (p) REVERT: B 54 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7442 (ptt90) REVERT: B 73 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7308 (tm-30) REVERT: B 303 HIS cc_start: 0.8580 (t-90) cc_final: 0.8266 (t-90) REVERT: B 359 ILE cc_start: 0.8440 (mt) cc_final: 0.8190 (mm) REVERT: B 385 SER cc_start: 0.8534 (t) cc_final: 0.8256 (p) REVERT: B 610 ASN cc_start: 0.7695 (m-40) cc_final: 0.7410 (m-40) outliers start: 19 outliers final: 19 residues processed: 218 average time/residue: 2.5042 time to fit residues: 587.6214 Evaluate side-chains 225 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 103 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9929 Z= 0.383 Angle : 0.553 5.531 13476 Z= 0.286 Chirality : 0.046 0.148 1438 Planarity : 0.004 0.067 1761 Dihedral : 7.834 96.613 1461 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.97 % Allowed : 18.31 % Favored : 79.72 % 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: -0.20 (0.24), residues: 1231 helix: -1.95 (0.61), residues: 71 sheet: 0.28 (0.22), residues: 536 loop : -0.16 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 187 HIS 0.005 0.001 HIS A 339 PHE 0.013 0.002 PHE A 115 TYR 0.014 0.002 TYR B 597 ARG 0.002 0.000 ARG A 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7787 (mp0) cc_final: 0.7482 (mp0) REVERT: A 159 GLU cc_start: 0.7203 (mp0) cc_final: 0.6981 (pm20) REVERT: A 225 ASP cc_start: 0.7343 (p0) cc_final: 0.7088 (p0) REVERT: A 228 ASN cc_start: 0.8605 (t0) cc_final: 0.8383 (t0) REVERT: A 478 ASP cc_start: 0.7571 (m-30) cc_final: 0.7296 (m-30) REVERT: A 534 VAL cc_start: 0.8852 (t) cc_final: 0.8556 (p) REVERT: B 41 SER cc_start: 0.7628 (m) cc_final: 0.7188 (p) REVERT: B 73 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7300 (tm-30) REVERT: B 303 HIS cc_start: 0.8565 (t-90) cc_final: 0.8291 (t-90) REVERT: B 359 ILE cc_start: 0.8452 (mt) cc_final: 0.8202 (mm) REVERT: B 385 SER cc_start: 0.8529 (t) cc_final: 0.8258 (p) REVERT: B 610 ASN cc_start: 0.7696 (m-40) cc_final: 0.7409 (m-40) outliers start: 20 outliers final: 19 residues processed: 215 average time/residue: 2.5137 time to fit residues: 581.6699 Evaluate side-chains 222 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.0980 chunk 89 optimal weight: 0.0570 chunk 14 optimal weight: 0.0000 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096340 restraints weight = 38566.380| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.55 r_work: 0.3215 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9929 Z= 0.189 Angle : 0.505 5.375 13476 Z= 0.261 Chirality : 0.045 0.150 1438 Planarity : 0.004 0.067 1761 Dihedral : 7.617 99.625 1461 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.67 % Allowed : 18.70 % Favored : 79.63 % 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: -0.02 (0.24), residues: 1231 helix: -1.67 (0.65), residues: 71 sheet: 0.39 (0.22), residues: 534 loop : -0.06 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 187 HIS 0.002 0.001 HIS A 339 PHE 0.010 0.001 PHE A 115 TYR 0.009 0.001 TYR A 444 ARG 0.002 0.000 ARG B 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10000.92 seconds wall clock time: 176 minutes 31.23 seconds (10591.23 seconds total)