Starting phenix.real_space_refine on Wed Feb 14 07:34:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/02_2024/6xmp_22260_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/02_2024/6xmp_22260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/02_2024/6xmp_22260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/02_2024/6xmp_22260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/02_2024/6xmp_22260_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/02_2024/6xmp_22260_trim_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 5576 2.51 5 N 1373 2.21 5 O 1559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A GLU 662": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 1079": "OE1" <-> "OE2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A GLU 1190": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8545 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8545 Unusual residues: {'LMT': 12} Classifications: {'peptide': 1086, 'undetermined': 12} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 48, 'TRANS': 1037, None: 12} Not linked: pdbres="LYS A1211 " pdbres="LMT A2001 " Not linked: pdbres="LMT A2001 " pdbres="LMT A2002 " Not linked: pdbres="LMT A2002 " pdbres="LMT A2003 " Not linked: pdbres="LMT A2003 " pdbres="LMT A2004 " Not linked: pdbres="LMT A2004 " pdbres="LMT A2005 " ... (remaining 7 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 594 Unresolved non-hydrogen dihedrals: 695 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 113 Time building chain proxies: 5.05, per 1000 atoms: 0.59 Number of scatterers: 8545 At special positions: 0 Unit cell: (83.22, 95.76, 137.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1559 8.00 N 1373 7.00 C 5576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 9 sheets defined 42.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 30 through 43 Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 58 through 77 Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.918A pdb=" N SER A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 154' Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.707A pdb=" N GLN A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 189 through 198 removed outlier: 3.586A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 219 through 249 removed outlier: 3.509A pdb=" N ALA A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 4.428A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 337 " --> pdb=" O ASP A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 337' Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 397 through 423 removed outlier: 3.885A pdb=" N TYR A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 442 removed outlier: 4.524A pdb=" N LEU A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 465 removed outlier: 4.003A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 Proline residue: A 476 - end of helix Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 656 through 659 No H-bonds generated for 'chain 'A' and resid 656 through 659' Processing helix chain 'A' and resid 679 through 688 Processing helix chain 'A' and resid 701 through 711 Processing helix chain 'A' and resid 754 through 757 No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 767 through 772 Processing helix chain 'A' and resid 779 through 784 removed outlier: 4.177A pdb=" N ARG A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 Processing helix chain 'A' and resid 821 through 826 removed outlier: 3.944A pdb=" N LYS A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 838 through 851 Processing helix chain 'A' and resid 973 through 1011 Processing helix chain 'A' and resid 1019 through 1036 removed outlier: 3.992A pdb=" N CYS A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A1034 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1083 Processing helix chain 'A' and resid 1100 through 1119 removed outlier: 3.740A pdb=" N VAL A1114 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1151 removed outlier: 3.859A pdb=" N GLY A1139 " --> pdb=" O GLY A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1161 Processing helix chain 'A' and resid 1169 through 1197 removed outlier: 4.050A pdb=" N ILE A1173 " --> pdb=" O ASP A1169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 90 removed outlier: 4.000A pdb=" N LEU A 17 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER A 15 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 100 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU A 17 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS A 98 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 111 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 116 through 120 removed outlier: 4.078A pdb=" N VAL A 118 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 136 through 138 removed outlier: 3.558A pdb=" N LEU A 136 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 145 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 138 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 143 " --> pdb=" O HIS A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 263 through 267 removed outlier: 4.700A pdb=" N ASN A 257 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU A 277 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 467 through 469 removed outlier: 7.106A pdb=" N VAL A 483 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS A 814 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYS A 485 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG A 692 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A 486 " --> pdb=" O ARG A 692 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 694 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 498 through 503 removed outlier: 3.799A pdb=" N VAL A 498 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU A 502 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 668 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 638 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A 668 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 636 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE A 670 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 634 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 600 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 593 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 578 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER A 594 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 576 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 719 through 723 removed outlier: 3.616A pdb=" N ASP A 722 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 764 through 766 removed outlier: 6.448A pdb=" N VAL A 788 " --> pdb=" O VAL A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 299 through 303 removed outlier: 4.122A pdb=" N SER A 299 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 347 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN A 303 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA A 345 " --> pdb=" O ASN A 303 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1014 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: 2.93 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2661 1.34 - 1.46: 1287 1.46 - 1.57: 4706 1.57 - 1.69: 0 1.69 - 1.80: 62 Bond restraints: 8716 Sorted by residual: bond pdb=" C7 LMT A2003 " pdb=" C8 LMT A2003 " ideal model delta sigma weight residual 1.529 1.440 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C5 LMT A2003 " pdb=" C6 LMT A2003 " ideal model delta sigma weight residual 1.527 1.438 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C7 LMT A2011 " pdb=" C8 LMT A2011 " ideal model delta sigma weight residual 1.529 1.450 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C6 LMT A2003 " pdb=" C7 LMT A2003 " ideal model delta sigma weight residual 1.527 1.448 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C7 LMT A2001 " pdb=" C8 LMT A2001 " ideal model delta sigma weight residual 1.529 1.456 0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 265 106.83 - 113.63: 4947 113.63 - 120.43: 3340 120.43 - 127.23: 3138 127.23 - 134.03: 84 Bond angle restraints: 11774 Sorted by residual: angle pdb=" C6 LMT A2003 " pdb=" C7 LMT A2003 " pdb=" C8 LMT A2003 " ideal model delta sigma weight residual 117.26 105.31 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C2 LMT A2003 " pdb=" C3 LMT A2003 " pdb=" C4 LMT A2003 " ideal model delta sigma weight residual 117.09 105.72 11.37 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C2 LMT A2004 " pdb=" C3 LMT A2004 " pdb=" C4 LMT A2004 " ideal model delta sigma weight residual 117.09 106.25 10.84 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C10 LMT A2011 " pdb=" C9 LMT A2011 " pdb=" C8 LMT A2011 " ideal model delta sigma weight residual 116.03 105.60 10.43 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C6 LMT A2008 " pdb=" C7 LMT A2008 " pdb=" C8 LMT A2008 " ideal model delta sigma weight residual 117.26 107.07 10.19 3.00e+00 1.11e-01 1.15e+01 ... (remaining 11769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4759 17.11 - 34.22: 430 34.22 - 51.33: 69 51.33 - 68.44: 15 68.44 - 85.55: 5 Dihedral angle restraints: 5278 sinusoidal: 2124 harmonic: 3154 Sorted by residual: dihedral pdb=" CA ARG A 760 " pdb=" C ARG A 760 " pdb=" N TYR A 761 " pdb=" CA TYR A 761 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ASP A 496 " pdb=" CB ASP A 496 " pdb=" CG ASP A 496 " pdb=" OD1 ASP A 496 " ideal model delta sinusoidal sigma weight residual -30.00 -88.30 58.30 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU A 420 " pdb=" CG GLU A 420 " pdb=" CD GLU A 420 " pdb=" OE1 GLU A 420 " ideal model delta sinusoidal sigma weight residual 0.00 -85.55 85.55 1 3.00e+01 1.11e-03 9.84e+00 ... (remaining 5275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1090 0.048 - 0.095: 215 0.095 - 0.143: 56 0.143 - 0.191: 5 0.191 - 0.238: 2 Chirality restraints: 1368 Sorted by residual: chirality pdb=" C5' LMT A2011 " pdb=" C4' LMT A2011 " pdb=" C6' LMT A2011 " pdb=" O5' LMT A2011 " both_signs ideal model delta sigma weight residual False -2.51 -2.27 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C5' LMT A2008 " pdb=" C4' LMT A2008 " pdb=" C6' LMT A2008 " pdb=" O5' LMT A2008 " both_signs ideal model delta sigma weight residual False -2.51 -2.29 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C4' LMT A2008 " pdb=" C3' LMT A2008 " pdb=" C5' LMT A2008 " pdb=" O1B LMT A2008 " both_signs ideal model delta sigma weight residual False -2.55 -2.73 0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 1365 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A1169 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" CG ASP A1169 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASP A1169 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A1169 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1093 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.60e+00 pdb=" CD GLU A1093 " 0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU A1093 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A1093 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 95 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" CD GLU A 95 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU A 95 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 95 " 0.019 2.00e-02 2.50e+03 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 630 2.73 - 3.28: 8371 3.28 - 3.82: 12909 3.82 - 4.36: 14154 4.36 - 4.90: 26148 Nonbonded interactions: 62212 Sorted by model distance: nonbonded pdb=" OG1 THR A 103 " pdb=" O ASN A 107 " model vdw 2.192 2.440 nonbonded pdb=" O SER A 690 " pdb=" OG SER A 690 " model vdw 2.286 2.440 nonbonded pdb=" O SER A 689 " pdb=" OG SER A 689 " model vdw 2.302 2.440 nonbonded pdb=" O SER A 154 " pdb=" OG SER A 154 " model vdw 2.316 2.440 nonbonded pdb=" NH2 ARG A 513 " pdb=" OG SER A 631 " model vdw 2.348 2.520 ... (remaining 62207 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.600 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 0.089 8716 Z= 0.472 Angle : 0.783 11.951 11774 Z= 0.350 Chirality : 0.043 0.238 1368 Planarity : 0.004 0.032 1467 Dihedral : 13.275 85.555 3236 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: -1.66 (0.23), residues: 1078 helix: -0.00 (0.22), residues: 467 sheet: -1.77 (0.36), residues: 149 loop : -1.98 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.008 0.001 HIS A 595 PHE 0.016 0.001 PHE A 405 TYR 0.008 0.001 TYR A 625 ARG 0.003 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.933 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2109 time to fit residues: 12.9768 Evaluate side-chains 25 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 261 ASN A 327 ASN A 533 HIS A 620 ASN A 776 HIS ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN A1089 GLN A1122 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8716 Z= 0.399 Angle : 0.596 7.153 11774 Z= 0.305 Chirality : 0.041 0.144 1368 Planarity : 0.003 0.025 1467 Dihedral : 7.977 59.304 1318 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.56 % Allowed : 12.04 % Favored : 87.40 % 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: -0.39 (0.25), residues: 1078 helix: 1.27 (0.24), residues: 470 sheet: -1.38 (0.40), residues: 146 loop : -1.49 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 787 HIS 0.006 0.001 HIS A 595 PHE 0.016 0.001 PHE A 226 TYR 0.010 0.001 TYR A1004 ARG 0.004 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.906 Fit side-chains REVERT: A 449 MET cc_start: 0.7351 (tpp) cc_final: 0.6799 (tpp) outliers start: 5 outliers final: 1 residues processed: 29 average time/residue: 0.1534 time to fit residues: 7.7328 Evaluate side-chains 26 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 595 HIS ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8716 Z= 0.284 Angle : 0.504 5.378 11774 Z= 0.262 Chirality : 0.040 0.142 1368 Planarity : 0.003 0.026 1467 Dihedral : 7.112 57.316 1318 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.34 % Allowed : 15.16 % Favored : 83.50 % 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 (0.25), residues: 1078 helix: 1.89 (0.24), residues: 469 sheet: -1.28 (0.38), residues: 152 loop : -1.40 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 218 HIS 0.005 0.001 HIS A 595 PHE 0.014 0.001 PHE A 405 TYR 0.010 0.001 TYR A1004 ARG 0.003 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 26 time to evaluate : 1.028 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 35 average time/residue: 0.1603 time to fit residues: 9.6305 Evaluate side-chains 32 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1182 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8716 Z= 0.208 Angle : 0.469 5.600 11774 Z= 0.242 Chirality : 0.039 0.150 1368 Planarity : 0.003 0.026 1467 Dihedral : 6.387 54.654 1318 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.56 % Allowed : 16.61 % Favored : 81.83 % 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: 0.47 (0.26), residues: 1078 helix: 2.20 (0.24), residues: 470 sheet: -1.12 (0.39), residues: 152 loop : -1.22 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 218 HIS 0.003 0.001 HIS A 785 PHE 0.014 0.001 PHE A 405 TYR 0.009 0.001 TYR A1004 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 0.899 Fit side-chains REVERT: A 249 MET cc_start: 0.7861 (mpp) cc_final: 0.7652 (mtm) outliers start: 14 outliers final: 6 residues processed: 39 average time/residue: 0.1650 time to fit residues: 10.8897 Evaluate side-chains 32 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1182 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8716 Z= 0.239 Angle : 0.482 5.954 11774 Z= 0.248 Chirality : 0.039 0.144 1368 Planarity : 0.003 0.026 1467 Dihedral : 6.151 53.848 1318 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.45 % Allowed : 17.39 % Favored : 80.16 % 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: 0.65 (0.26), residues: 1078 helix: 2.40 (0.24), residues: 463 sheet: -0.97 (0.40), residues: 152 loop : -1.17 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 787 HIS 0.003 0.001 HIS A 785 PHE 0.014 0.001 PHE A 405 TYR 0.009 0.001 TYR A1004 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 27 time to evaluate : 1.060 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 47 average time/residue: 0.1496 time to fit residues: 12.0482 Evaluate side-chains 39 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1182 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8716 Z= 0.219 Angle : 0.476 7.044 11774 Z= 0.243 Chirality : 0.039 0.150 1368 Planarity : 0.003 0.028 1467 Dihedral : 6.030 55.643 1318 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.34 % Allowed : 18.28 % Favored : 79.38 % 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: 0.78 (0.26), residues: 1078 helix: 2.49 (0.24), residues: 464 sheet: -0.87 (0.40), residues: 152 loop : -1.10 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.003 0.001 HIS A1069 PHE 0.015 0.001 PHE A 405 TYR 0.009 0.001 TYR A1004 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 26 time to evaluate : 1.216 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 46 average time/residue: 0.1551 time to fit residues: 12.1467 Evaluate side-chains 42 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 26 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1182 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 0.0070 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.0040 overall best weight: 1.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8716 Z= 0.170 Angle : 0.461 7.870 11774 Z= 0.233 Chirality : 0.038 0.174 1368 Planarity : 0.003 0.027 1467 Dihedral : 5.799 57.347 1318 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.34 % Allowed : 18.62 % Favored : 79.04 % 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: 0.88 (0.26), residues: 1078 helix: 2.55 (0.24), residues: 465 sheet: -0.79 (0.40), residues: 151 loop : -1.04 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 787 HIS 0.003 0.001 HIS A1069 PHE 0.014 0.001 PHE A 405 TYR 0.009 0.001 TYR A1004 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 26 time to evaluate : 0.892 Fit side-chains REVERT: A 249 MET cc_start: 0.7897 (mpp) cc_final: 0.7695 (mtm) outliers start: 21 outliers final: 15 residues processed: 45 average time/residue: 0.1468 time to fit residues: 11.3147 Evaluate side-chains 41 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 26 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1182 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8716 Z= 0.125 Angle : 0.455 8.699 11774 Z= 0.227 Chirality : 0.038 0.175 1368 Planarity : 0.003 0.027 1467 Dihedral : 5.484 58.872 1318 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.34 % Allowed : 20.18 % Favored : 78.48 % 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: 1.03 (0.26), residues: 1078 helix: 2.70 (0.24), residues: 461 sheet: -0.65 (0.40), residues: 151 loop : -0.98 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.003 0.000 HIS A1069 PHE 0.013 0.001 PHE A 405 TYR 0.010 0.001 TYR A1004 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 28 time to evaluate : 1.063 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 38 average time/residue: 0.1583 time to fit residues: 10.3378 Evaluate side-chains 36 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1180 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 0.0870 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 64 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 0.0070 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8716 Z= 0.106 Angle : 0.435 8.380 11774 Z= 0.216 Chirality : 0.037 0.165 1368 Planarity : 0.003 0.027 1467 Dihedral : 5.000 57.909 1318 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.00 % Allowed : 20.29 % Favored : 78.71 % 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: 1.19 (0.26), residues: 1078 helix: 2.84 (0.24), residues: 461 sheet: -0.49 (0.41), residues: 145 loop : -0.92 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 558 HIS 0.003 0.000 HIS A1069 PHE 0.011 0.001 PHE A 405 TYR 0.010 0.001 TYR A1004 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 1.033 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 0.1989 time to fit residues: 13.5968 Evaluate side-chains 38 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 99 optimal weight: 0.0570 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8716 Z= 0.119 Angle : 0.451 9.558 11774 Z= 0.218 Chirality : 0.037 0.150 1368 Planarity : 0.003 0.028 1467 Dihedral : 4.917 57.296 1318 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.78 % Allowed : 20.62 % Favored : 78.60 % 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: 1.29 (0.26), residues: 1078 helix: 2.93 (0.24), residues: 460 sheet: -0.44 (0.41), residues: 145 loop : -0.87 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 787 HIS 0.003 0.000 HIS A1069 PHE 0.011 0.001 PHE A 405 TYR 0.009 0.001 TYR A1004 ARG 0.002 0.000 ARG A 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 1.023 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 39 average time/residue: 0.1542 time to fit residues: 10.2913 Evaluate side-chains 40 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.044094 restraints weight = 34207.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.045858 restraints weight = 15750.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.047044 restraints weight = 9806.978| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8716 Z= 0.251 Angle : 0.501 9.455 11774 Z= 0.250 Chirality : 0.039 0.158 1368 Planarity : 0.003 0.028 1467 Dihedral : 5.404 58.407 1318 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.11 % Allowed : 20.29 % Favored : 78.60 % 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: 1.15 (0.26), residues: 1078 helix: 2.79 (0.24), residues: 462 sheet: -0.72 (0.39), residues: 157 loop : -0.85 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 218 HIS 0.002 0.001 HIS A1069 PHE 0.013 0.001 PHE A1164 TYR 0.009 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1472.65 seconds wall clock time: 27 minutes 49.98 seconds (1669.98 seconds total)