Starting phenix.real_space_refine on Fri Nov 17 10:51:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/11_2023/8b14_15802_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/11_2023/8b14_15802.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/11_2023/8b14_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_15802/11_2023/8b14_15802_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/11_2023/8b14_15802_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/11_2023/8b14_15802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/11_2023/8b14_15802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/11_2023/8b14_15802_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/11_2023/8b14_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 8.12, per 1000 atoms: 0.43 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: 15.51 Conformation dependent library (CDL) restraints added in 1.9 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: 3.94 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: 10.01 Time building geometry restraints manager: 16.02 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: 7468 34.98 - 69.95: 212 69.95 - 104.93: 34 104.93 - 139.90: 4 139.90 - 174.88: 1 Dihedral angle restraints: 7719 sinusoidal: 3479 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 7716 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: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.290 Extract box with map and model: 18.390 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 66.780 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.420 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 221 average time/residue: 2.4594 time to fit residues: 586.8491 Evaluate side-chains 190 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.3632 time to fit residues: 2.2166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 362 GLN A 592 ASN A 690 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: 0.8004 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 9929 Z= 0.461 Angle : 0.610 5.434 13476 Z= 0.320 Chirality : 0.049 0.156 1438 Planarity : 0.004 0.047 1761 Dihedral : 10.822 113.456 1459 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: 0.04 (0.24), residues: 1231 helix: -2.33 (0.56), residues: 70 sheet: 0.65 (0.23), residues: 534 loop : -0.15 (0.24), residues: 627 *********************** 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 222 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 209 average time/residue: 2.5077 time to fit residues: 565.9056 Evaluate side-chains 211 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 8 residues processed: 11 average time/residue: 0.5769 time to fit residues: 10.4242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 76 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 89 optimal weight: 0.2980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 ASN A 714 GLN B 115 GLN B 238 ASN B 360 ASN B 475 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9929 Z= 0.255 Angle : 0.530 4.817 13476 Z= 0.276 Chirality : 0.046 0.151 1438 Planarity : 0.003 0.058 1761 Dihedral : 9.400 105.101 1459 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 16.14 % Favored : 81.79 % 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: -2.05 (0.60), residues: 70 sheet: 0.65 (0.23), residues: 534 loop : -0.07 (0.25), residues: 627 *********************** 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 218 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 209 average time/residue: 2.5061 time to fit residues: 563.9914 Evaluate side-chains 206 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.3137 time to fit residues: 3.1954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 360 ASN B 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 9929 Z= 0.482 Angle : 0.593 5.271 13476 Z= 0.307 Chirality : 0.048 0.155 1438 Planarity : 0.004 0.063 1761 Dihedral : 8.862 104.092 1459 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.95 % Allowed : 16.04 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1231 helix: -2.26 (0.58), residues: 71 sheet: 0.42 (0.22), residues: 535 loop : -0.19 (0.25), residues: 625 *********************** 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 224 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 212 average time/residue: 2.5152 time to fit residues: 574.2753 Evaluate side-chains 214 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 0.8004 time to fit residues: 9.5795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 ASN A 714 GLN B 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9929 Z= 0.321 Angle : 0.547 5.646 13476 Z= 0.283 Chirality : 0.046 0.153 1438 Planarity : 0.004 0.063 1761 Dihedral : 8.510 102.614 1459 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.17 % Allowed : 16.44 % 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: -0.11 (0.24), residues: 1231 helix: -2.06 (0.60), residues: 71 sheet: 0.37 (0.22), residues: 536 loop : -0.12 (0.25), residues: 624 *********************** 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 220 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 211 average time/residue: 2.6048 time to fit residues: 592.7855 Evaluate side-chains 212 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 1.2295 time to fit residues: 10.6392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 714 GLN B 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9929 Z= 0.344 Angle : 0.549 5.316 13476 Z= 0.283 Chirality : 0.046 0.158 1438 Planarity : 0.004 0.063 1761 Dihedral : 8.269 102.392 1459 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.97 % Allowed : 17.32 % Favored : 80.71 % 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: -0.15 (0.24), residues: 1231 helix: -1.91 (0.62), residues: 70 sheet: 0.30 (0.22), residues: 538 loop : -0.13 (0.25), residues: 623 *********************** 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 220 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 212 average time/residue: 2.5001 time to fit residues: 570.7148 Evaluate side-chains 216 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 5 average time/residue: 0.8858 time to fit residues: 7.1542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 47 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8000 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 9929 Z= 0.433 Angle : 0.574 5.428 13476 Z= 0.296 Chirality : 0.047 0.155 1438 Planarity : 0.004 0.063 1761 Dihedral : 8.173 99.670 1459 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.46 % Allowed : 17.32 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1231 helix: -1.96 (0.62), residues: 70 sheet: 0.24 (0.22), residues: 538 loop : -0.16 (0.25), residues: 623 *********************** 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 224 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 213 average time/residue: 2.5313 time to fit residues: 580.3245 Evaluate side-chains 216 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.6555 time to fit residues: 6.2713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.0370 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 11 optimal weight: 0.0980 chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A 592 ASN A 714 GLN B 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9929 Z= 0.195 Angle : 0.514 5.565 13476 Z= 0.265 Chirality : 0.045 0.157 1438 Planarity : 0.003 0.063 1761 Dihedral : 7.878 102.068 1459 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.67 % Allowed : 18.21 % 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: -0.08 (0.24), residues: 1231 helix: -1.69 (0.65), residues: 70 sheet: 0.32 (0.22), residues: 535 loop : -0.07 (0.25), residues: 626 *********************** 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 218 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 214 average time/residue: 2.4683 time to fit residues: 568.5325 Evaluate side-chains 216 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.3070 time to fit residues: 2.5312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 66 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 72 optimal weight: 0.0980 chunk 116 optimal weight: 0.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 714 GLN B 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9929 Z= 0.243 Angle : 0.521 5.357 13476 Z= 0.267 Chirality : 0.045 0.149 1438 Planarity : 0.003 0.062 1761 Dihedral : 7.723 101.722 1459 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.48 % Allowed : 18.70 % Favored : 79.82 % 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: -0.05 (0.24), residues: 1231 helix: -1.61 (0.65), residues: 70 sheet: 0.33 (0.22), residues: 535 loop : -0.04 (0.25), residues: 626 *********************** 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 222 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 218 average time/residue: 2.4901 time to fit residues: 585.9730 Evaluate side-chains 219 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.8237 time to fit residues: 4.7108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 77 optimal weight: 0.1980 chunk 103 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 165 GLN A 714 GLN B 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9929 Z= 0.398 Angle : 0.563 5.434 13476 Z= 0.289 Chirality : 0.046 0.150 1438 Planarity : 0.004 0.063 1761 Dihedral : 7.744 98.470 1459 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.18 % Allowed : 18.90 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1231 helix: -1.80 (0.63), residues: 70 sheet: 0.25 (0.22), residues: 538 loop : -0.11 (0.25), residues: 623 ********************** 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 218 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 206 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 217 average time/residue: 2.5454 time to fit residues: 595.6669 Evaluate side-chains 216 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.8047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 714 GLN B 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.094673 restraints weight = 38836.214| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.55 r_work: 0.3189 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 9929 Z= 0.492 Angle : 0.598 6.487 13476 Z= 0.308 Chirality : 0.048 0.152 1438 Planarity : 0.004 0.063 1761 Dihedral : 7.798 95.647 1459 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.87 % Allowed : 18.70 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1231 helix: -1.94 (0.62), residues: 69 sheet: 0.20 (0.22), residues: 538 loop : -0.17 (0.25), residues: 624 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9984.81 seconds wall clock time: 176 minutes 41.71 seconds (10601.71 seconds total)