Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 09:41:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/10_2023/6xmp_22260_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/10_2023/6xmp_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_22260/10_2023/6xmp_22260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/10_2023/6xmp_22260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/10_2023/6xmp_22260_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmp_22260/10_2023/6xmp_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 143 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: 4.95, per 1000 atoms: 0.58 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: 3.23 Conformation dependent library (CDL) restraints added in 1.4 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: 2.16 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: 2.81 Time building geometry restraints manager: 3.52 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: 4715 17.11 - 34.22: 428 34.22 - 51.33: 67 51.33 - 68.44: 15 68.44 - 85.55: 5 Dihedral angle restraints: 5230 sinusoidal: 2076 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 5227 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.940 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.250 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- 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 : 13.273 85.555 3188 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 *********************** 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 : 1.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2133 time to fit residues: 13.3783 Evaluate side-chains 25 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3874 ------------------------------------------------------------------------------- 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: 0.8478 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8716 Z= 0.398 Angle : 0.595 7.240 11774 Z= 0.304 Chirality : 0.041 0.143 1368 Planarity : 0.003 0.025 1467 Dihedral : 7.869 59.023 1270 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.56 % Allowed : 11.71 % Favored : 87.74 % 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: -0.45 (0.25), residues: 1078 helix: 1.19 (0.24), residues: 477 sheet: -1.37 (0.39), residues: 149 loop : -1.55 (0.26), residues: 452 *********************** 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 : 1.001 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.1710 time to fit residues: 8.7480 Evaluate side-chains 27 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0915 time to fit residues: 1.7826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** 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: 0.8456 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8716 Z= 0.259 Angle : 0.495 5.417 11774 Z= 0.256 Chirality : 0.039 0.143 1368 Planarity : 0.003 0.026 1467 Dihedral : 7.033 58.289 1270 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.00 % Allowed : 14.83 % Favored : 84.17 % 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: 1.87 (0.24), residues: 469 sheet: -1.28 (0.38), residues: 152 loop : -1.38 (0.26), residues: 457 *********************** 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 35 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 1.028 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 32 average time/residue: 0.1620 time to fit residues: 9.0058 Evaluate side-chains 30 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0850 time to fit residues: 1.9491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 0.0170 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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: 0.8387 moved from start: 0.1499 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= 0.126 Angle : 0.439 5.705 11774 Z= 0.224 Chirality : 0.038 0.143 1368 Planarity : 0.003 0.025 1467 Dihedral : 6.028 57.554 1270 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.67 % Allowed : 16.05 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1078 helix: 2.39 (0.24), residues: 464 sheet: -0.95 (0.40), residues: 146 loop : -1.20 (0.26), residues: 468 *********************** 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 35 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 1.028 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 34 average time/residue: 0.2084 time to fit residues: 11.2737 Evaluate side-chains 27 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0890 time to fit residues: 1.5413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.8416 moved from start: 0.1593 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= 0.173 Angle : 0.448 6.600 11774 Z= 0.228 Chirality : 0.038 0.144 1368 Planarity : 0.003 0.025 1467 Dihedral : 5.735 54.766 1270 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.89 % Allowed : 17.17 % Favored : 81.94 % 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: 0.87 (0.26), residues: 1078 helix: 2.56 (0.24), residues: 464 sheet: -0.79 (0.40), residues: 152 loop : -1.06 (0.27), residues: 462 *********************** 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 36 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 1.010 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 35 average time/residue: 0.1645 time to fit residues: 10.0182 Evaluate side-chains 29 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0806 time to fit residues: 1.6679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 101 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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: 0.8369 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8716 Z= 0.119 Angle : 0.434 6.960 11774 Z= 0.219 Chirality : 0.038 0.162 1368 Planarity : 0.003 0.026 1467 Dihedral : 5.388 56.914 1270 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.33 % Allowed : 17.95 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1078 helix: 2.69 (0.24), residues: 463 sheet: -0.50 (0.42), residues: 145 loop : -0.97 (0.27), residues: 470 *********************** 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 31 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 1.029 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 31 average time/residue: 0.1738 time to fit residues: 9.3021 Evaluate side-chains 29 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0956 time to fit residues: 1.7032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.8432 moved from start: 0.1773 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= 0.216 Angle : 0.465 6.914 11774 Z= 0.236 Chirality : 0.038 0.142 1368 Planarity : 0.003 0.027 1467 Dihedral : 5.455 56.775 1270 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.00 % Allowed : 17.50 % Favored : 81.49 % 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: 1.09 (0.26), residues: 1078 helix: 2.71 (0.24), residues: 464 sheet: -0.61 (0.40), residues: 152 loop : -0.93 (0.27), residues: 462 *********************** 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 35 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 1.000 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 35 average time/residue: 0.1602 time to fit residues: 9.7466 Evaluate side-chains 31 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0813 time to fit residues: 2.0921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 82 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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: 0.8385 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8716 Z= 0.130 Angle : 0.451 7.837 11774 Z= 0.224 Chirality : 0.038 0.141 1368 Planarity : 0.003 0.027 1467 Dihedral : 5.219 59.026 1270 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.33 % Allowed : 18.06 % Favored : 81.61 % 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: 1.14 (0.26), residues: 1078 helix: 2.71 (0.24), residues: 466 sheet: -0.52 (0.41), residues: 150 loop : -0.89 (0.27), residues: 462 *********************** 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 31 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 1.027 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 30 average time/residue: 0.1721 time to fit residues: 9.0067 Evaluate side-chains 27 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 30 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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: 0.8449 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8716 Z= 0.263 Angle : 0.497 7.934 11774 Z= 0.251 Chirality : 0.039 0.142 1368 Planarity : 0.003 0.028 1467 Dihedral : 5.473 58.379 1270 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.33 % Allowed : 18.28 % Favored : 81.38 % 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: 1.10 (0.26), residues: 1078 helix: 2.71 (0.24), residues: 463 sheet: -0.69 (0.40), residues: 157 loop : -0.86 (0.28), residues: 458 *********************** 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 30 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.986 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.1768 time to fit residues: 9.1977 Evaluate side-chains 29 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1262 time to fit residues: 1.5719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.0040 chunk 26 optimal weight: 0.4980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 129 GLN ** 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: 0.8383 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8716 Z= 0.122 Angle : 0.473 10.913 11774 Z= 0.230 Chirality : 0.038 0.213 1368 Planarity : 0.003 0.028 1467 Dihedral : 5.157 58.791 1270 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 18.51 % Favored : 81.49 % 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: 1.22 (0.26), residues: 1078 helix: 2.79 (0.24), residues: 464 sheet: -0.49 (0.41), residues: 150 loop : -0.84 (0.28), residues: 464 ********************** 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 33 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1754 time to fit residues: 9.8944 Evaluate side-chains 29 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.058125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.045429 restraints weight = 33901.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.047234 restraints weight = 15494.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.048450 restraints weight = 9586.216| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8716 Z= 0.177 Angle : 0.479 10.848 11774 Z= 0.234 Chirality : 0.038 0.212 1368 Planarity : 0.003 0.028 1467 Dihedral : 5.161 58.747 1270 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 19.18 % Favored : 80.82 % 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: 1.22 (0.26), residues: 1078 helix: 2.80 (0.24), residues: 464 sheet: -0.57 (0.40), residues: 156 loop : -0.81 (0.28), residues: 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1432.21 seconds wall clock time: 27 minutes 8.20 seconds (1628.20 seconds total)