Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 12:22:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/10_2023/8b14_15802_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/10_2023/8b14_15802.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/10_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_15802/10_2023/8b14_15802_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/10_2023/8b14_15802_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/10_2023/8b14_15802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/10_2023/8b14_15802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/10_2023/8b14_15802_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b14_15802/10_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 8.39, per 1000 atoms: 0.45 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: 15.56 Conformation dependent library (CDL) restraints added in 1.6 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: 2.79 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: 9.56 Time building geometry restraints manager: 16.09 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: 7443 34.98 - 69.95: 204 69.95 - 104.93: 31 104.93 - 139.90: 3 139.90 - 174.88: 1 Dihedral angle restraints: 7682 sinusoidal: 3442 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 7679 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: 5.430 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: 18.510 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 68.340 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.100 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:22.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.520 ------------------------------------------------------------------------------- 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 : 16.802 174.880 3547 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 : 1.394 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: 2.4256 time to fit residues: 578.4758 Evaluate side-chains 190 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.3685 time to fit residues: 2.4003 ------------------------------------------------------------------------------- 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: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9929 Z= 0.451 Angle : 0.606 5.420 13476 Z= 0.317 Chirality : 0.049 0.157 1438 Planarity : 0.004 0.048 1761 Dihedral : 9.179 111.270 1422 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.76 % Allowed : 15.85 % 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: -2.33 (0.56), residues: 70 sheet: 0.75 (0.23), residues: 524 loop : -0.18 (0.24), residues: 637 *********************** 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 223 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 210 average time/residue: 2.4740 time to fit residues: 561.3358 Evaluate side-chains 213 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 1.469 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 8 residues processed: 11 average time/residue: 0.5597 time to fit residues: 10.0852 ------------------------------------------------------------------------------- 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: 0.3980 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 0.0770 chunk 89 optimal weight: 0.3980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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: 0.7987 moved from start: 0.1823 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= 0.264 Angle : 0.533 4.785 13476 Z= 0.278 Chirality : 0.045 0.151 1438 Planarity : 0.004 0.057 1761 Dihedral : 7.889 87.609 1422 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.17 % Allowed : 16.04 % 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: 0.07 (0.24), residues: 1231 helix: -2.08 (0.60), residues: 70 sheet: 0.65 (0.23), residues: 525 loop : -0.13 (0.25), residues: 636 *********************** 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 221 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 213 average time/residue: 2.4286 time to fit residues: 558.9070 Evaluate side-chains 209 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.3331 time to fit residues: 3.3698 ------------------------------------------------------------------------------- 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: 0.9980 chunk 58 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 9929 Z= 0.534 Angle : 0.612 5.525 13476 Z= 0.317 Chirality : 0.049 0.152 1438 Planarity : 0.004 0.063 1761 Dihedral : 7.313 75.021 1422 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.15 % Allowed : 15.65 % 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: -0.20 (0.24), residues: 1231 helix: -2.37 (0.56), residues: 71 sheet: 0.40 (0.22), residues: 535 loop : -0.23 (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 228 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 215 average time/residue: 2.4735 time to fit residues: 573.3943 Evaluate side-chains 215 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 0.7952 time to fit residues: 9.6492 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 0 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7999 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9929 Z= 0.389 Angle : 0.566 5.555 13476 Z= 0.294 Chirality : 0.047 0.152 1438 Planarity : 0.004 0.063 1761 Dihedral : 6.995 72.060 1422 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.46 % Allowed : 16.44 % Favored : 81.10 % 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: -2.27 (0.58), residues: 71 sheet: 0.32 (0.22), residues: 538 loop : -0.18 (0.25), residues: 622 *********************** 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 225 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 20 residues processed: 214 average time/residue: 2.4518 time to fit residues: 565.3765 Evaluate side-chains 218 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 8 average time/residue: 0.5719 time to fit residues: 7.2299 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9929 Z= 0.381 Angle : 0.559 5.285 13476 Z= 0.290 Chirality : 0.046 0.157 1438 Planarity : 0.004 0.064 1761 Dihedral : 6.734 69.944 1422 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.17 % Allowed : 17.22 % Favored : 80.61 % 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: -2.10 (0.60), residues: 70 sheet: 0.25 (0.22), residues: 538 loop : -0.16 (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 227 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 219 average time/residue: 2.5003 time to fit residues: 590.6561 Evaluate side-chains 219 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 4 average time/residue: 1.0511 time to fit residues: 6.7741 ------------------------------------------------------------------------------- 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: 0.3980 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 714 GLN B 475 GLN B 631 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2409 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= 0.418 Angle : 0.572 5.592 13476 Z= 0.296 Chirality : 0.047 0.156 1438 Planarity : 0.004 0.064 1761 Dihedral : 6.614 67.899 1422 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.76 % Allowed : 17.42 % 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: -0.26 (0.24), residues: 1231 helix: -2.07 (0.60), residues: 70 sheet: 0.21 (0.22), residues: 536 loop : -0.17 (0.25), residues: 625 *********************** 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 231 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 219 average time/residue: 2.4495 time to fit residues: 578.1382 Evaluate side-chains 218 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 1.605 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.9358 time to fit residues: 8.5067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.8209 > 50: distance: 12 - 22: 33.287 distance: 22 - 23: 20.620 distance: 23 - 24: 8.872 distance: 23 - 26: 16.813 distance: 23 - 31: 21.588 distance: 24 - 25: 31.011 distance: 24 - 41: 8.935 distance: 26 - 27: 11.405 distance: 26 - 32: 14.818 distance: 26 - 33: 24.229 distance: 27 - 28: 14.650 distance: 27 - 29: 9.595 distance: 27 - 34: 15.056 distance: 28 - 35: 3.868 distance: 28 - 37: 3.173 distance: 29 - 40: 7.747 distance: 41 - 42: 10.578 distance: 41 - 47: 11.655 distance: 42 - 43: 7.407 distance: 42 - 45: 21.345 distance: 42 - 48: 8.603 distance: 43 - 44: 5.560 distance: 43 - 55: 47.145 distance: 45 - 46: 18.389 distance: 45 - 49: 3.687 distance: 45 - 50: 5.586 distance: 46 - 47: 17.503 distance: 46 - 51: 8.417 distance: 46 - 52: 9.598 distance: 47 - 53: 12.213 distance: 47 - 54: 12.287 distance: 55 - 56: 6.320 distance: 55 - 64: 13.347 distance: 56 - 57: 9.990 distance: 56 - 59: 13.701 distance: 56 - 65: 24.489 distance: 57 - 58: 19.673 distance: 57 - 77: 21.990 distance: 59 - 60: 13.063 distance: 59 - 66: 17.623 distance: 59 - 67: 9.708 distance: 60 - 61: 8.588 distance: 60 - 68: 3.238 distance: 60 - 69: 13.772 distance: 61 - 62: 8.050 distance: 61 - 70: 12.419 distance: 61 - 71: 9.498 distance: 62 - 72: 4.518 distance: 62 - 73: 5.169 distance: 77 - 78: 16.253 distance: 77 - 86: 10.665 distance: 78 - 79: 33.694 distance: 78 - 81: 22.135 distance: 78 - 87: 19.652 distance: 79 - 80: 7.803 distance: 79 - 92: 11.328 distance: 81 - 82: 20.120 distance: 81 - 88: 9.755 distance: 81 - 89: 13.064 distance: 82 - 83: 6.269 distance: 82 - 90: 21.060 distance: 82 - 91: 11.621 distance: 83 - 84: 8.233 distance: 83 - 85: 6.979 distance: 92 - 93: 22.732 distance: 93 - 94: 23.188 distance: 93 - 97: 19.276 distance: 93 - 98: 17.787 distance: 94 - 95: 37.537 distance: 94 - 99: 23.331 distance: 99 - 100: 21.311 distance: 99 - 106: 18.789 distance: 100 - 101: 35.783 distance: 100 - 103: 26.671 distance: 100 - 107: 9.887 distance: 101 - 102: 16.572 distance: 101 - 113: 35.594 distance: 103 - 104: 17.172 distance: 103 - 105: 16.614 distance: 103 - 108: 12.360 distance: 104 - 109: 7.265 distance: 105 - 111: 19.691 distance: 105 - 112: 10.440 distance: 113 - 114: 28.221 distance: 113 - 120: 17.862 distance: 114 - 115: 43.811 distance: 114 - 117: 33.658 distance: 114 - 121: 9.903 distance: 115 - 116: 39.912 distance: 115 - 129: 49.808 distance: 117 - 118: 37.661 distance: 117 - 119: 30.438 distance: 118 - 123: 14.014 distance: 118 - 124: 12.996 distance: 118 - 125: 7.166 distance: 119 - 126: 12.724 distance: 119 - 127: 7.766 distance: 119 - 128: 9.487 distance: 129 - 130: 35.683 distance: 129 - 138: 34.314 distance: 130 - 131: 39.250 distance: 130 - 133: 25.437 distance: 130 - 139: 30.972 distance: 131 - 132: 48.231 distance: 131 - 144: 35.201 distance: 133 - 134: 40.036 distance: 133 - 140: 26.522 distance: 133 - 141: 48.392 distance: 134 - 135: 31.785 distance: 134 - 142: 35.838 distance: 134 - 143: 17.964 distance: 135 - 136: 8.785 distance: 135 - 137: 44.429 distance: 144 - 145: 11.484 distance: 144 - 150: 11.122 distance: 145 - 146: 10.373 distance: 145 - 148: 18.140 distance: 145 - 151: 46.225 distance: 146 - 147: 6.101 distance: 146 - 158: 8.246 distance: 148 - 149: 16.606 distance: 148 - 152: 33.175 distance: 148 - 153: 37.872 distance: 149 - 150: 12.224 distance: 149 - 154: 24.704 distance: 149 - 155: 43.086 distance: 150 - 156: 17.589 distance: 150 - 157: 25.579 distance: 158 - 159: 21.533 distance: 158 - 166: 4.771 distance: 159 - 160: 31.641 distance: 159 - 162: 26.012 distance: 159 - 167: 9.252 distance: 160 - 161: 12.204 distance: 160 - 177: 18.271 distance: 162 - 163: 6.298 distance: 162 - 168: 18.813 distance: 162 - 169: 14.058 distance: 163 - 164: 17.637 distance: 163 - 165: 15.212 distance: 163 - 170: 8.716 distance: 164 - 171: 7.900 distance: 164 - 172: 3.703 distance: 164 - 173: 3.040 distance: 165 - 174: 5.094 distance: 165 - 175: 6.045