Starting phenix.real_space_refine on Mon Mar 11 18:34:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/03_2024/6nyb_0541_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/03_2024/6nyb_0541.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/03_2024/6nyb_0541_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/03_2024/6nyb_0541_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/03_2024/6nyb_0541_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/03_2024/6nyb_0541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/03_2024/6nyb_0541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/03_2024/6nyb_0541_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/03_2024/6nyb_0541_updated.pdb" } resolution = 4.1 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= 0.007 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: 9 Type Number sf(0) Gaussians I 1 10.91 5 Zn 2 6.06 5 P 7 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 5583 2.51 5 N 1527 2.21 5 O 1668 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "C ARG 55": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2819 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 2 Chain: "B" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2258 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 16, 'TRANS': 272} Chain breaks: 1 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {' MG': 1, 'ADP': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 136 SG CYS A 248 61.072 29.426 55.042 1.00 69.52 S ATOM 161 SG CYS A 251 62.989 27.854 57.470 1.00 79.60 S ATOM 343 SG CYS A 272 60.523 25.561 55.470 1.00113.58 S ATOM 249 SG CYS A 261 53.756 37.009 46.317 1.00107.92 S ATOM 271 SG CYS A 264 53.994 38.015 49.372 1.00114.35 S ATOM 401 SG CYS A 280 50.374 39.002 48.986 1.00149.39 S Time building chain proxies: 5.30, per 1000 atoms: 0.60 Number of scatterers: 8842 At special positions: 0 Unit cell: (111.3, 93.28, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) I 1 52.95 Zn 2 29.99 S 52 16.00 P 7 15.00 Mg 1 11.99 F 1 9.00 O 1668 8.00 N 1527 7.00 C 5583 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 272 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 251 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 280 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 235 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 261 " Number of angles added : 3 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 5 sheets defined 53.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 492 through 507 removed outlier: 3.651A pdb=" N GLN A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 550 through 569 Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 635 through 651 Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.548A pdb=" N LEU A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.601A pdb=" N ALA A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.537A pdb=" N GLN B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.529A pdb=" N LYS B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 183 removed outlier: 3.787A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 243 through 258 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 332 through 341 Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.516A pdb=" N ALA B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.758A pdb=" N THR C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 69 removed outlier: 3.916A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 52 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 101 Processing helix chain 'C' and resid 112 through 130 Processing helix chain 'C' and resid 138 through 159 removed outlier: 3.578A pdb=" N GLU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 180 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'D' and resid 3 through 15 Processing helix chain 'D' and resid 20 through 30 removed outlier: 3.950A pdb=" N VAL D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 67 removed outlier: 3.814A pdb=" N LEU D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 removed outlier: 3.579A pdb=" N GLU D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 removed outlier: 3.932A pdb=" N LEU D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 132 removed outlier: 3.784A pdb=" N GLU D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 159 removed outlier: 3.984A pdb=" N ASP D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 185 through 201 Processing helix chain 'D' and resid 213 through 229 Processing sheet with id= A, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= B, first strand: chain 'A' and resid 527 through 530 removed outlier: 6.520A pdb=" N LYS A 473 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG A 462 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 582 through 585 Processing sheet with id= D, first strand: chain 'B' and resid 129 through 135 removed outlier: 6.853A pdb=" N CYS B 142 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 132 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 140 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR B 134 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 92 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER B 86 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 70 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 196 through 198 407 hydrogen bonds defined for protein. 1212 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: 2.25 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 3024 1.37 - 1.55: 5889 1.55 - 1.74: 11 1.74 - 1.92: 84 1.92 - 2.11: 2 Bond restraints: 9010 Sorted by residual: bond pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C5 AGS A 801 " pdb=" C6 AGS A 801 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" PG AGS A 801 " pdb=" S1G AGS A 801 " ideal model delta sigma weight residual 1.949 2.074 -0.125 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C8 AGS A 801 " pdb=" N7 AGS A 801 " ideal model delta sigma weight residual 1.311 1.358 -0.047 1.00e-02 1.00e+04 2.22e+01 ... (remaining 9005 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.64: 265 106.64 - 114.14: 5035 114.14 - 121.63: 4262 121.63 - 129.12: 2541 129.12 - 136.62: 54 Bond angle restraints: 12157 Sorted by residual: angle pdb=" C5 AGS A 801 " pdb=" C4 AGS A 801 " pdb=" N3 AGS A 801 " ideal model delta sigma weight residual 126.80 119.45 7.35 7.41e-01 1.82e+00 9.84e+01 angle pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " pdb=" N7 AGS A 801 " ideal model delta sigma weight residual 110.73 106.42 4.31 4.52e-01 4.89e+00 9.11e+01 angle pdb=" C5 AGS A 801 " pdb=" N7 AGS A 801 " pdb=" C8 AGS A 801 " ideal model delta sigma weight residual 103.67 107.48 -3.81 4.26e-01 5.51e+00 7.99e+01 angle pdb=" N1 AGS A 801 " pdb=" C2 AGS A 801 " pdb=" N3 AGS A 801 " ideal model delta sigma weight residual 128.80 123.21 5.59 8.41e-01 1.41e+00 4.42e+01 angle pdb=" C4 AGS A 801 " pdb=" N9 AGS A 801 " pdb=" C8 AGS A 801 " ideal model delta sigma weight residual 105.70 108.67 -2.97 4.55e-01 4.83e+00 4.25e+01 ... (remaining 12152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.85: 5034 18.85 - 37.70: 343 37.70 - 56.56: 95 56.56 - 75.41: 22 75.41 - 94.26: 5 Dihedral angle restraints: 5499 sinusoidal: 2293 harmonic: 3206 Sorted by residual: dihedral pdb=" C ASP A 587 " pdb=" N ASP A 587 " pdb=" CA ASP A 587 " pdb=" CB ASP A 587 " ideal model delta harmonic sigma weight residual -122.60 -139.54 16.94 0 2.50e+00 1.60e-01 4.59e+01 dihedral pdb=" N ASP A 587 " pdb=" C ASP A 587 " pdb=" CA ASP A 587 " pdb=" CB ASP A 587 " ideal model delta harmonic sigma weight residual 122.80 138.29 -15.49 0 2.50e+00 1.60e-01 3.84e+01 dihedral pdb=" C ASP B 190 " pdb=" N ASP B 190 " pdb=" CA ASP B 190 " pdb=" CB ASP B 190 " ideal model delta harmonic sigma weight residual -122.60 -135.64 13.04 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 1209 0.138 - 0.277: 121 0.277 - 0.415: 2 0.415 - 0.554: 1 0.554 - 0.692: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA ASP A 587 " pdb=" N ASP A 587 " pdb=" C ASP A 587 " pdb=" CB ASP A 587 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASP B 190 " pdb=" N ASP B 190 " pdb=" C ASP B 190 " pdb=" CB ASP B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA ASP A 576 " pdb=" N ASP A 576 " pdb=" C ASP A 576 " pdb=" CB ASP A 576 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 1331 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 726 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.21e+00 pdb=" C ARG A 726 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG A 726 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 727 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 628 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C GLN A 628 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN A 628 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 629 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 104 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C HIS D 104 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS D 104 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 105 " -0.014 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.65: 89 2.65 - 3.23: 7986 3.23 - 3.80: 13946 3.80 - 4.38: 19090 4.38 - 4.96: 31467 Nonbonded interactions: 72578 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb="MG MG B 602 " model vdw 2.070 2.170 nonbonded pdb=" O3P SEP A 729 " pdb=" NH2 ARG D 56 " model vdw 2.247 2.520 nonbonded pdb=" O PHE A 468 " pdb=" N ASN A 486 " model vdw 2.256 2.520 nonbonded pdb=" NZ LYS D 88 " pdb=" OE2 GLU D 92 " model vdw 2.350 2.520 nonbonded pdb=" O SER A 520 " pdb=" O GLN A 524 " model vdw 2.367 3.040 ... (remaining 72573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid \ 202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ h 230)) selection = chain 'D' } 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: 0.510 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: 2.170 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.850 Find NCS groups from input model: 0.340 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.014 0.125 9010 Z= 0.876 Angle : 1.755 12.235 12157 Z= 1.314 Chirality : 0.091 0.692 1334 Planarity : 0.003 0.029 1548 Dihedral : 14.451 94.262 3425 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.39 % Favored : 94.43 % Rotamer: Outliers : 3.66 % Allowed : 5.02 % Favored : 91.32 % Cbeta Deviations : 0.29 % 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: -3.02 (0.22), residues: 1077 helix: -1.43 (0.18), residues: 596 sheet: -2.52 (0.58), residues: 57 loop : -2.65 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.007 0.002 HIS A 269 PHE 0.015 0.002 PHE A 250 TYR 0.020 0.002 TYR C 179 ARG 0.004 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 406 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 LYS cc_start: 0.8456 (tttt) cc_final: 0.8076 (tttm) REVERT: A 501 GLU cc_start: 0.8098 (tp30) cc_final: 0.7565 (tp30) REVERT: A 544 ILE cc_start: 0.8968 (pt) cc_final: 0.8048 (mp) REVERT: A 640 TYR cc_start: 0.8918 (t80) cc_final: 0.8599 (t80) REVERT: A 698 LYS cc_start: 0.8373 (mmtp) cc_final: 0.8081 (mmmm) REVERT: A 715 GLU cc_start: 0.8006 (tt0) cc_final: 0.7763 (tp30) REVERT: A 723 LYS cc_start: 0.5281 (OUTLIER) cc_final: 0.4903 (pttt) REVERT: B 63 LEU cc_start: 0.6488 (mt) cc_final: 0.5635 (mp) REVERT: B 114 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8679 (tt0) REVERT: B 130 TYR cc_start: 0.9032 (m-80) cc_final: 0.7894 (m-10) REVERT: B 146 MET cc_start: 0.8515 (mmm) cc_final: 0.8089 (mmm) REVERT: B 160 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8106 (ptm-80) REVERT: B 163 GLU cc_start: 0.7441 (tt0) cc_final: 0.6981 (tm-30) REVERT: B 195 ASN cc_start: 0.8701 (m-40) cc_final: 0.8292 (m-40) REVERT: B 207 CYS cc_start: 0.9338 (p) cc_final: 0.8575 (t) REVERT: B 230 MET cc_start: 0.7535 (tpp) cc_final: 0.7271 (mmt) REVERT: B 253 LEU cc_start: 0.9635 (mt) cc_final: 0.9292 (mm) REVERT: B 255 GLU cc_start: 0.8018 (tt0) cc_final: 0.7725 (tt0) REVERT: B 308 MET cc_start: 0.8177 (mmp) cc_final: 0.7733 (mmm) REVERT: B 333 GLU cc_start: 0.9430 (mp0) cc_final: 0.9086 (mp0) REVERT: B 337 PHE cc_start: 0.9124 (t80) cc_final: 0.8881 (t80) REVERT: B 341 CYS cc_start: 0.8925 (m) cc_final: 0.8248 (m) REVERT: B 342 LEU cc_start: 0.8780 (mt) cc_final: 0.8453 (mt) REVERT: B 358 HIS cc_start: 0.6902 (t-90) cc_final: 0.6398 (t-90) REVERT: B 374 TRP cc_start: 0.8372 (t60) cc_final: 0.7892 (t60) REVERT: C 14 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8252 (tm-30) REVERT: C 27 LYS cc_start: 0.8849 (tttt) cc_final: 0.8644 (ttpp) REVERT: C 30 THR cc_start: 0.8892 (m) cc_final: 0.8667 (t) REVERT: C 100 LEU cc_start: 0.8404 (mt) cc_final: 0.7985 (mt) REVERT: C 149 TYR cc_start: 0.8207 (m-10) cc_final: 0.7835 (m-10) REVERT: C 179 TYR cc_start: 0.9029 (t80) cc_final: 0.8768 (t80) REVERT: C 194 GLN cc_start: 0.8542 (tt0) cc_final: 0.8222 (tm-30) REVERT: D 167 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8015 (ttt-90) outliers start: 35 outliers final: 8 residues processed: 426 average time/residue: 0.2472 time to fit residues: 136.4560 Evaluate side-chains 244 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 235 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN B 87 HIS B 243 GLN C 8 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9010 Z= 0.202 Angle : 0.650 9.763 12157 Z= 0.332 Chirality : 0.041 0.179 1334 Planarity : 0.005 0.064 1548 Dihedral : 6.885 89.082 1232 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.21 % Allowed : 2.72 % Favored : 97.07 % 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: -0.77 (0.24), residues: 1077 helix: 0.54 (0.20), residues: 601 sheet: -1.68 (0.64), residues: 54 loop : -1.89 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 476 HIS 0.014 0.002 HIS A 269 PHE 0.027 0.002 PHE B 371 TYR 0.019 0.002 TYR A 656 ARG 0.018 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.8446 (mtp) cc_final: 0.7957 (mtt) REVERT: A 501 GLU cc_start: 0.8352 (tp30) cc_final: 0.7947 (tp30) REVERT: A 505 LEU cc_start: 0.9244 (mt) cc_final: 0.8531 (mt) REVERT: A 544 ILE cc_start: 0.8390 (pt) cc_final: 0.7649 (tt) REVERT: A 564 MET cc_start: 0.8258 (tpt) cc_final: 0.8013 (tpp) REVERT: A 591 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7678 (mtpt) REVERT: A 608 HIS cc_start: 0.6066 (p90) cc_final: 0.5703 (m90) REVERT: A 617 ILE cc_start: 0.8739 (pt) cc_final: 0.8499 (pt) REVERT: A 640 TYR cc_start: 0.9180 (t80) cc_final: 0.8874 (t80) REVERT: A 715 GLU cc_start: 0.7963 (tt0) cc_final: 0.7619 (tp30) REVERT: B 114 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8745 (tt0) REVERT: B 146 MET cc_start: 0.8936 (mmm) cc_final: 0.8123 (mmm) REVERT: B 160 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.8242 (ptm-80) REVERT: B 180 LEU cc_start: 0.8841 (mt) cc_final: 0.8639 (mt) REVERT: B 181 ARG cc_start: 0.8441 (mmp-170) cc_final: 0.8140 (mmm160) REVERT: B 186 ILE cc_start: 0.7724 (mm) cc_final: 0.7509 (mm) REVERT: B 195 ASN cc_start: 0.8683 (m-40) cc_final: 0.7681 (t0) REVERT: B 197 LEU cc_start: 0.8372 (mm) cc_final: 0.7909 (mm) REVERT: B 233 GLU cc_start: 0.6753 (pp20) cc_final: 0.5963 (pp20) REVERT: B 242 VAL cc_start: 0.8600 (m) cc_final: 0.8169 (m) REVERT: B 319 ASN cc_start: 0.9212 (t0) cc_final: 0.8834 (p0) REVERT: B 341 CYS cc_start: 0.8379 (m) cc_final: 0.8166 (m) REVERT: B 342 LEU cc_start: 0.8870 (mt) cc_final: 0.8610 (mt) REVERT: C 100 LEU cc_start: 0.8515 (mt) cc_final: 0.8277 (mt) REVERT: C 111 ASN cc_start: 0.8596 (t0) cc_final: 0.8333 (t0) REVERT: C 194 GLN cc_start: 0.8508 (tt0) cc_final: 0.8084 (tm-30) REVERT: D 26 MET cc_start: 0.9071 (mmp) cc_final: 0.8816 (tpp) REVERT: D 59 TRP cc_start: 0.9236 (t60) cc_final: 0.8897 (t60) REVERT: D 167 ARG cc_start: 0.8573 (ttt180) cc_final: 0.7871 (ttt-90) outliers start: 2 outliers final: 1 residues processed: 291 average time/residue: 0.2370 time to fit residues: 91.3448 Evaluate side-chains 203 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 ASN B 87 HIS B 119 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9010 Z= 0.217 Angle : 0.609 10.926 12157 Z= 0.308 Chirality : 0.041 0.167 1334 Planarity : 0.005 0.057 1548 Dihedral : 6.356 95.470 1232 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1077 helix: 1.05 (0.21), residues: 603 sheet: -0.63 (0.69), residues: 44 loop : -1.60 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 374 HIS 0.006 0.001 HIS A 568 PHE 0.025 0.002 PHE C 174 TYR 0.023 0.002 TYR A 673 ARG 0.011 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.8813 (mtp) cc_final: 0.8550 (mtt) REVERT: A 501 GLU cc_start: 0.8415 (tp30) cc_final: 0.7790 (tp30) REVERT: A 565 ASP cc_start: 0.8395 (t0) cc_final: 0.8141 (t0) REVERT: A 591 LYS cc_start: 0.8334 (mmtt) cc_final: 0.8104 (mtpt) REVERT: A 608 HIS cc_start: 0.6240 (p90) cc_final: 0.5718 (m90) REVERT: A 640 TYR cc_start: 0.9202 (t80) cc_final: 0.8797 (t80) REVERT: A 699 LYS cc_start: 0.8489 (mttp) cc_final: 0.8257 (mmtm) REVERT: A 715 GLU cc_start: 0.7844 (tt0) cc_final: 0.7593 (tp30) REVERT: B 114 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8750 (tt0) REVERT: B 130 TYR cc_start: 0.8370 (m-10) cc_final: 0.7944 (m-10) REVERT: B 146 MET cc_start: 0.9070 (mmm) cc_final: 0.8308 (mmm) REVERT: B 180 LEU cc_start: 0.8960 (mt) cc_final: 0.8582 (mt) REVERT: B 181 ARG cc_start: 0.8431 (mmp-170) cc_final: 0.8027 (mmm160) REVERT: B 195 ASN cc_start: 0.8742 (m-40) cc_final: 0.8230 (m-40) REVERT: B 197 LEU cc_start: 0.8401 (mm) cc_final: 0.7964 (mm) REVERT: B 233 GLU cc_start: 0.7174 (pp20) cc_final: 0.6637 (pp20) REVERT: B 242 VAL cc_start: 0.8663 (m) cc_final: 0.8276 (p) REVERT: B 249 MET cc_start: 0.9276 (tmm) cc_final: 0.8994 (tmm) REVERT: B 319 ASN cc_start: 0.9270 (t0) cc_final: 0.8840 (t0) REVERT: B 337 PHE cc_start: 0.9312 (t80) cc_final: 0.8894 (t80) REVERT: B 341 CYS cc_start: 0.8673 (m) cc_final: 0.8252 (m) REVERT: B 342 LEU cc_start: 0.8584 (mt) cc_final: 0.8201 (mt) REVERT: B 374 TRP cc_start: 0.8691 (t60) cc_final: 0.8287 (t60) REVERT: C 74 ARG cc_start: 0.8232 (ptt180) cc_final: 0.7565 (ptt180) REVERT: C 100 LEU cc_start: 0.8566 (mt) cc_final: 0.8310 (mt) REVERT: C 111 ASN cc_start: 0.8499 (t0) cc_final: 0.8196 (t0) REVERT: C 196 PHE cc_start: 0.8526 (t80) cc_final: 0.8279 (t80) REVERT: C 218 MET cc_start: 0.9179 (mmm) cc_final: 0.8373 (mmm) REVERT: D 26 MET cc_start: 0.9211 (mmp) cc_final: 0.8910 (mpp) REVERT: D 59 TRP cc_start: 0.9292 (t60) cc_final: 0.8968 (t60) REVERT: D 224 ASN cc_start: 0.8887 (m-40) cc_final: 0.8582 (m-40) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.1838 time to fit residues: 65.8349 Evaluate side-chains 194 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9010 Z= 0.332 Angle : 0.677 11.689 12157 Z= 0.344 Chirality : 0.043 0.170 1334 Planarity : 0.005 0.059 1548 Dihedral : 6.402 96.991 1232 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.21 % Allowed : 2.41 % Favored : 97.38 % 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: -0.02 (0.26), residues: 1077 helix: 1.00 (0.21), residues: 609 sheet: -0.49 (0.68), residues: 44 loop : -1.45 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 247 HIS 0.008 0.001 HIS B 87 PHE 0.061 0.003 PHE B 360 TYR 0.021 0.002 TYR A 673 ARG 0.008 0.001 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.9006 (mtp) cc_final: 0.8694 (mtt) REVERT: A 501 GLU cc_start: 0.8430 (tp30) cc_final: 0.8013 (tp30) REVERT: A 505 LEU cc_start: 0.9326 (mt) cc_final: 0.8589 (mt) REVERT: A 517 MET cc_start: 0.8333 (mmt) cc_final: 0.7940 (mmt) REVERT: A 564 MET cc_start: 0.8161 (tpp) cc_final: 0.7915 (tpp) REVERT: A 565 ASP cc_start: 0.8526 (t0) cc_final: 0.8203 (t0) REVERT: A 608 HIS cc_start: 0.6335 (p90) cc_final: 0.5885 (m170) REVERT: A 640 TYR cc_start: 0.9272 (t80) cc_final: 0.8732 (t80) REVERT: A 715 GLU cc_start: 0.7909 (tt0) cc_final: 0.7663 (tp30) REVERT: B 94 MET cc_start: 0.4186 (pmm) cc_final: 0.3894 (pmm) REVERT: B 108 ARG cc_start: 0.9173 (ptt180) cc_final: 0.8662 (ptp90) REVERT: B 133 PHE cc_start: 0.8591 (t80) cc_final: 0.8162 (t80) REVERT: B 146 MET cc_start: 0.9068 (mmm) cc_final: 0.8348 (mmm) REVERT: B 160 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8294 (ptm-80) REVERT: B 180 LEU cc_start: 0.9023 (mt) cc_final: 0.8693 (mt) REVERT: B 187 MET cc_start: 0.6193 (ttm) cc_final: 0.5965 (ttm) REVERT: B 195 ASN cc_start: 0.8837 (m-40) cc_final: 0.8620 (m-40) REVERT: B 207 CYS cc_start: 0.8960 (p) cc_final: 0.8073 (t) REVERT: B 233 GLU cc_start: 0.7237 (pp20) cc_final: 0.6457 (pp20) REVERT: B 249 MET cc_start: 0.9243 (tmm) cc_final: 0.9015 (tmm) REVERT: B 256 MET cc_start: 0.9009 (mtm) cc_final: 0.8808 (mtm) REVERT: B 319 ASN cc_start: 0.9296 (t0) cc_final: 0.8828 (t0) REVERT: B 337 PHE cc_start: 0.9148 (t80) cc_final: 0.8764 (t80) REVERT: B 342 LEU cc_start: 0.8548 (mt) cc_final: 0.8235 (mt) REVERT: C 74 ARG cc_start: 0.8295 (ptt180) cc_final: 0.7704 (ptt180) REVERT: C 78 MET cc_start: 0.7995 (ptp) cc_final: 0.7770 (ptp) REVERT: C 100 LEU cc_start: 0.8586 (mt) cc_final: 0.8331 (mt) REVERT: C 218 MET cc_start: 0.9271 (mmm) cc_final: 0.8711 (mmm) REVERT: D 26 MET cc_start: 0.9203 (mmp) cc_final: 0.8868 (mpp) REVERT: D 59 TRP cc_start: 0.9303 (t60) cc_final: 0.8951 (t60) REVERT: D 224 ASN cc_start: 0.8895 (m-40) cc_final: 0.8640 (m110) outliers start: 2 outliers final: 1 residues processed: 237 average time/residue: 0.2290 time to fit residues: 73.5730 Evaluate side-chains 175 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 512 ASN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9010 Z= 0.233 Angle : 0.621 10.823 12157 Z= 0.313 Chirality : 0.041 0.180 1334 Planarity : 0.004 0.067 1548 Dihedral : 6.256 100.265 1232 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1077 helix: 1.22 (0.22), residues: 602 sheet: -0.95 (0.67), residues: 43 loop : -1.35 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 374 HIS 0.009 0.001 HIS B 188 PHE 0.056 0.002 PHE C 174 TYR 0.023 0.002 TYR A 673 ARG 0.005 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.9071 (mtp) cc_final: 0.8846 (mtt) REVERT: A 485 LEU cc_start: 0.9188 (mt) cc_final: 0.8978 (mt) REVERT: A 501 GLU cc_start: 0.8434 (tp30) cc_final: 0.7814 (tp30) REVERT: A 517 MET cc_start: 0.8208 (mmt) cc_final: 0.7813 (mmt) REVERT: A 564 MET cc_start: 0.8028 (tpp) cc_final: 0.7661 (tpp) REVERT: A 565 ASP cc_start: 0.8418 (t0) cc_final: 0.8092 (t0) REVERT: A 591 LYS cc_start: 0.8463 (mmtt) cc_final: 0.7979 (mttp) REVERT: A 608 HIS cc_start: 0.6243 (p90) cc_final: 0.5823 (m170) REVERT: A 640 TYR cc_start: 0.9182 (t80) cc_final: 0.8940 (t80) REVERT: A 715 GLU cc_start: 0.7881 (tt0) cc_final: 0.7558 (tp30) REVERT: B 94 MET cc_start: 0.4230 (pmm) cc_final: 0.3793 (pmm) REVERT: B 114 GLU cc_start: 0.8681 (tt0) cc_final: 0.8345 (tm-30) REVERT: B 133 PHE cc_start: 0.8711 (t80) cc_final: 0.8365 (t80) REVERT: B 146 MET cc_start: 0.9103 (mmm) cc_final: 0.8354 (mmm) REVERT: B 180 LEU cc_start: 0.9084 (mt) cc_final: 0.8777 (mt) REVERT: B 195 ASN cc_start: 0.8753 (m-40) cc_final: 0.8471 (m-40) REVERT: B 197 LEU cc_start: 0.8380 (mm) cc_final: 0.7856 (mm) REVERT: B 209 PHE cc_start: 0.9288 (p90) cc_final: 0.9081 (p90) REVERT: B 233 GLU cc_start: 0.7371 (pp20) cc_final: 0.6649 (pp20) REVERT: B 249 MET cc_start: 0.9187 (tmm) cc_final: 0.8971 (tmm) REVERT: B 319 ASN cc_start: 0.9287 (t0) cc_final: 0.8786 (t0) REVERT: B 337 PHE cc_start: 0.9079 (t80) cc_final: 0.8715 (t80) REVERT: B 341 CYS cc_start: 0.8490 (m) cc_final: 0.8239 (m) REVERT: B 374 TRP cc_start: 0.8734 (t60) cc_final: 0.8502 (t60) REVERT: C 74 ARG cc_start: 0.8316 (ptt180) cc_final: 0.7742 (ptt180) REVERT: C 100 LEU cc_start: 0.8624 (mt) cc_final: 0.8374 (mt) REVERT: C 207 ASN cc_start: 0.8872 (p0) cc_final: 0.8626 (p0) REVERT: C 218 MET cc_start: 0.9267 (mmm) cc_final: 0.8667 (mmm) REVERT: D 26 MET cc_start: 0.9211 (mmp) cc_final: 0.8970 (tpp) REVERT: D 59 TRP cc_start: 0.9283 (t60) cc_final: 0.8917 (t60) REVERT: D 224 ASN cc_start: 0.8915 (m-40) cc_final: 0.8596 (m-40) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2090 time to fit residues: 64.2182 Evaluate side-chains 179 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9010 Z= 0.174 Angle : 0.587 11.227 12157 Z= 0.294 Chirality : 0.040 0.179 1334 Planarity : 0.004 0.041 1548 Dihedral : 6.189 103.025 1232 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % 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: 0.34 (0.26), residues: 1077 helix: 1.35 (0.22), residues: 602 sheet: -0.89 (0.73), residues: 43 loop : -1.29 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 247 HIS 0.011 0.001 HIS A 235 PHE 0.048 0.002 PHE B 360 TYR 0.023 0.002 TYR A 656 ARG 0.005 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.9062 (mtp) cc_final: 0.8813 (mtt) REVERT: A 485 LEU cc_start: 0.9282 (mt) cc_final: 0.9069 (mt) REVERT: A 501 GLU cc_start: 0.8436 (tp30) cc_final: 0.7749 (tp30) REVERT: A 564 MET cc_start: 0.7919 (tpp) cc_final: 0.7511 (tpp) REVERT: A 565 ASP cc_start: 0.8282 (t0) cc_final: 0.8004 (t0) REVERT: A 608 HIS cc_start: 0.6155 (p90) cc_final: 0.5776 (m170) REVERT: A 640 TYR cc_start: 0.9110 (t80) cc_final: 0.8894 (t80) REVERT: A 715 GLU cc_start: 0.7778 (tt0) cc_final: 0.7505 (tp30) REVERT: B 94 MET cc_start: 0.4642 (pmm) cc_final: 0.4200 (pmm) REVERT: B 114 GLU cc_start: 0.8590 (tt0) cc_final: 0.8366 (tm-30) REVERT: B 146 MET cc_start: 0.9047 (mmm) cc_final: 0.8296 (mmm) REVERT: B 180 LEU cc_start: 0.9114 (mt) cc_final: 0.8859 (mt) REVERT: B 197 LEU cc_start: 0.8298 (mm) cc_final: 0.7811 (mm) REVERT: B 209 PHE cc_start: 0.9276 (p90) cc_final: 0.8887 (p90) REVERT: B 233 GLU cc_start: 0.7342 (pp20) cc_final: 0.6614 (pp20) REVERT: B 249 MET cc_start: 0.9200 (tmm) cc_final: 0.8915 (tmm) REVERT: B 319 ASN cc_start: 0.9262 (t0) cc_final: 0.8738 (t0) REVERT: B 341 CYS cc_start: 0.8516 (m) cc_final: 0.8307 (m) REVERT: C 100 LEU cc_start: 0.8586 (mt) cc_final: 0.8024 (mt) REVERT: C 203 LEU cc_start: 0.8999 (mt) cc_final: 0.8732 (mt) REVERT: C 207 ASN cc_start: 0.8936 (p0) cc_final: 0.8681 (p0) REVERT: C 218 MET cc_start: 0.9255 (mmm) cc_final: 0.8971 (mmm) REVERT: C 228 TRP cc_start: 0.8926 (m-10) cc_final: 0.8492 (m-90) REVERT: D 59 TRP cc_start: 0.9271 (t60) cc_final: 0.8874 (t60) REVERT: D 224 ASN cc_start: 0.8847 (m-40) cc_final: 0.8544 (m-40) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.1951 time to fit residues: 62.0954 Evaluate side-chains 172 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.0470 chunk 103 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 30.0000 chunk 47 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9010 Z= 0.260 Angle : 0.661 12.542 12157 Z= 0.330 Chirality : 0.042 0.178 1334 Planarity : 0.004 0.040 1548 Dihedral : 6.212 106.699 1232 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 0.28 (0.26), residues: 1077 helix: 1.33 (0.22), residues: 599 sheet: -0.69 (0.68), residues: 43 loop : -1.38 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 374 HIS 0.017 0.002 HIS D 164 PHE 0.045 0.002 PHE B 334 TYR 0.020 0.002 TYR A 673 ARG 0.004 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.9092 (mtp) cc_final: 0.8855 (mtt) REVERT: A 501 GLU cc_start: 0.8496 (tp30) cc_final: 0.8005 (tp30) REVERT: A 505 LEU cc_start: 0.9347 (mt) cc_final: 0.8598 (mt) REVERT: A 564 MET cc_start: 0.8025 (tpp) cc_final: 0.7648 (tpp) REVERT: A 565 ASP cc_start: 0.8394 (t0) cc_final: 0.8178 (t0) REVERT: A 591 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8190 (mtmt) REVERT: A 608 HIS cc_start: 0.6247 (p90) cc_final: 0.5852 (m170) REVERT: A 640 TYR cc_start: 0.9207 (t80) cc_final: 0.8468 (t80) REVERT: B 94 MET cc_start: 0.4545 (pmm) cc_final: 0.4079 (pmm) REVERT: B 133 PHE cc_start: 0.8708 (t80) cc_final: 0.8327 (t80) REVERT: B 146 MET cc_start: 0.9128 (mmm) cc_final: 0.8375 (mmm) REVERT: B 180 LEU cc_start: 0.9108 (mt) cc_final: 0.8868 (mt) REVERT: B 187 MET cc_start: 0.6489 (ttm) cc_final: 0.6101 (ttm) REVERT: B 195 ASN cc_start: 0.8345 (m110) cc_final: 0.7868 (m-40) REVERT: B 197 LEU cc_start: 0.8228 (mm) cc_final: 0.7778 (mm) REVERT: B 209 PHE cc_start: 0.9065 (p90) cc_final: 0.8776 (p90) REVERT: B 233 GLU cc_start: 0.7430 (pp20) cc_final: 0.6683 (pp20) REVERT: B 249 MET cc_start: 0.9251 (tmm) cc_final: 0.8941 (tmm) REVERT: B 319 ASN cc_start: 0.9214 (t0) cc_final: 0.8667 (t0) REVERT: B 334 PHE cc_start: 0.9166 (t80) cc_final: 0.8955 (t80) REVERT: B 341 CYS cc_start: 0.8570 (m) cc_final: 0.8349 (m) REVERT: C 100 LEU cc_start: 0.8679 (mt) cc_final: 0.8428 (mt) REVERT: C 111 ASN cc_start: 0.8584 (t0) cc_final: 0.8260 (t0) REVERT: C 203 LEU cc_start: 0.9062 (mt) cc_final: 0.8853 (mt) REVERT: C 207 ASN cc_start: 0.8886 (p0) cc_final: 0.8548 (p0) REVERT: D 59 TRP cc_start: 0.9300 (t60) cc_final: 0.8899 (t60) REVERT: D 167 ARG cc_start: 0.8810 (ttt180) cc_final: 0.8551 (ttt180) REVERT: D 224 ASN cc_start: 0.8896 (m-40) cc_final: 0.8593 (m-40) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1973 time to fit residues: 57.8087 Evaluate side-chains 169 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9010 Z= 0.326 Angle : 0.702 12.224 12157 Z= 0.353 Chirality : 0.043 0.229 1334 Planarity : 0.004 0.040 1548 Dihedral : 6.337 108.904 1232 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 0.19 (0.26), residues: 1077 helix: 1.22 (0.22), residues: 598 sheet: -0.71 (0.70), residues: 41 loop : -1.35 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 374 HIS 0.015 0.002 HIS D 164 PHE 0.041 0.002 PHE C 174 TYR 0.026 0.002 TYR C 178 ARG 0.005 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8479 (tp30) cc_final: 0.8049 (tp30) REVERT: A 505 LEU cc_start: 0.9333 (mt) cc_final: 0.8613 (mt) REVERT: A 564 MET cc_start: 0.7903 (tpp) cc_final: 0.7679 (tpp) REVERT: A 591 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8231 (mttp) REVERT: A 608 HIS cc_start: 0.6288 (p90) cc_final: 0.6021 (m170) REVERT: A 640 TYR cc_start: 0.9283 (t80) cc_final: 0.8557 (t80) REVERT: A 734 ASN cc_start: 0.7696 (p0) cc_final: 0.7489 (p0) REVERT: B 94 MET cc_start: 0.4562 (pmm) cc_final: 0.4138 (pmm) REVERT: B 133 PHE cc_start: 0.8813 (t80) cc_final: 0.8430 (t80) REVERT: B 146 MET cc_start: 0.9164 (mmm) cc_final: 0.8291 (mmm) REVERT: B 157 LYS cc_start: 0.9399 (mttt) cc_final: 0.9128 (tptp) REVERT: B 180 LEU cc_start: 0.9177 (mt) cc_final: 0.8934 (mt) REVERT: B 187 MET cc_start: 0.6813 (ttm) cc_final: 0.6366 (ttm) REVERT: B 195 ASN cc_start: 0.8400 (m110) cc_final: 0.7987 (m-40) REVERT: B 209 PHE cc_start: 0.8713 (p90) cc_final: 0.8403 (p90) REVERT: B 233 GLU cc_start: 0.7440 (pp20) cc_final: 0.6657 (pp20) REVERT: B 249 MET cc_start: 0.9237 (tmm) cc_final: 0.8947 (tmm) REVERT: B 319 ASN cc_start: 0.9191 (t0) cc_final: 0.8625 (t0) REVERT: B 334 PHE cc_start: 0.9206 (t80) cc_final: 0.8967 (t80) REVERT: B 341 CYS cc_start: 0.8625 (m) cc_final: 0.8311 (m) REVERT: C 111 ASN cc_start: 0.8642 (t0) cc_final: 0.8301 (t0) REVERT: C 179 TYR cc_start: 0.9244 (t80) cc_final: 0.8938 (t80) REVERT: C 207 ASN cc_start: 0.8996 (p0) cc_final: 0.8581 (p0) REVERT: C 218 MET cc_start: 0.9230 (mmm) cc_final: 0.8493 (mmm) REVERT: C 228 TRP cc_start: 0.8995 (m-10) cc_final: 0.8413 (m-90) REVERT: D 59 TRP cc_start: 0.9297 (t60) cc_final: 0.8908 (t60) REVERT: D 224 ASN cc_start: 0.8933 (m-40) cc_final: 0.8603 (m-40) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2117 time to fit residues: 58.8174 Evaluate side-chains 157 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 57 optimal weight: 0.0030 chunk 41 optimal weight: 0.2980 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9010 Z= 0.166 Angle : 0.640 10.359 12157 Z= 0.323 Chirality : 0.041 0.183 1334 Planarity : 0.004 0.042 1548 Dihedral : 6.165 111.104 1232 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.10 % Allowed : 0.63 % Favored : 99.27 % 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: 0.41 (0.26), residues: 1077 helix: 1.45 (0.22), residues: 595 sheet: -0.85 (0.72), residues: 39 loop : -1.29 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 374 HIS 0.010 0.001 HIS D 164 PHE 0.027 0.002 PHE D 174 TYR 0.029 0.002 TYR D 178 ARG 0.004 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8373 (tp30) cc_final: 0.7808 (tp30) REVERT: A 512 ASN cc_start: 0.8450 (m-40) cc_final: 0.8009 (m-40) REVERT: A 591 LYS cc_start: 0.8628 (mmtt) cc_final: 0.7973 (mttp) REVERT: A 638 ASP cc_start: 0.8068 (t0) cc_final: 0.7757 (t0) REVERT: A 703 GLU cc_start: 0.8555 (tt0) cc_final: 0.7951 (tm-30) REVERT: B 94 MET cc_start: 0.4370 (pmm) cc_final: 0.3947 (pmm) REVERT: B 133 PHE cc_start: 0.8734 (t80) cc_final: 0.8334 (t80) REVERT: B 146 MET cc_start: 0.9002 (mmm) cc_final: 0.8186 (mmm) REVERT: B 157 LYS cc_start: 0.9373 (mttt) cc_final: 0.9046 (tptt) REVERT: B 180 LEU cc_start: 0.9117 (mt) cc_final: 0.8909 (mt) REVERT: B 187 MET cc_start: 0.6549 (ttm) cc_final: 0.6021 (ttm) REVERT: B 195 ASN cc_start: 0.8551 (m110) cc_final: 0.7884 (m-40) REVERT: B 209 PHE cc_start: 0.8705 (p90) cc_final: 0.8378 (p90) REVERT: B 233 GLU cc_start: 0.7333 (pp20) cc_final: 0.6599 (pp20) REVERT: B 249 MET cc_start: 0.9189 (tmm) cc_final: 0.8890 (tmm) REVERT: B 319 ASN cc_start: 0.9058 (t0) cc_final: 0.8445 (t0) REVERT: B 334 PHE cc_start: 0.9184 (t80) cc_final: 0.8930 (t80) REVERT: B 341 CYS cc_start: 0.8595 (m) cc_final: 0.8259 (m) REVERT: C 111 ASN cc_start: 0.8651 (t0) cc_final: 0.8346 (t0) REVERT: C 179 TYR cc_start: 0.9209 (t80) cc_final: 0.8913 (t80) REVERT: C 207 ASN cc_start: 0.8968 (p0) cc_final: 0.8499 (p0) REVERT: C 218 MET cc_start: 0.9281 (mmm) cc_final: 0.8652 (mmm) REVERT: C 228 TRP cc_start: 0.8805 (m-10) cc_final: 0.8291 (m-90) REVERT: D 59 TRP cc_start: 0.9245 (t60) cc_final: 0.8855 (t60) REVERT: D 224 ASN cc_start: 0.8845 (m-40) cc_final: 0.8604 (m-40) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1969 time to fit residues: 63.6153 Evaluate side-chains 167 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.0570 chunk 70 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9010 Z= 0.209 Angle : 0.662 10.650 12157 Z= 0.332 Chirality : 0.042 0.183 1334 Planarity : 0.004 0.040 1548 Dihedral : 6.114 113.770 1232 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.45 (0.26), residues: 1077 helix: 1.48 (0.22), residues: 595 sheet: -0.63 (0.71), residues: 41 loop : -1.29 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 374 HIS 0.009 0.001 HIS D 164 PHE 0.022 0.002 PHE B 360 TYR 0.028 0.002 TYR C 178 ARG 0.006 0.000 ARG C 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8358 (tp30) cc_final: 0.7973 (tp30) REVERT: A 505 LEU cc_start: 0.9295 (mt) cc_final: 0.8637 (mt) REVERT: A 506 ARG cc_start: 0.7868 (tpt170) cc_final: 0.7381 (tpp-160) REVERT: A 591 LYS cc_start: 0.8599 (mmtt) cc_final: 0.7933 (mttp) REVERT: A 638 ASP cc_start: 0.8016 (t0) cc_final: 0.7628 (t0) REVERT: B 94 MET cc_start: 0.4366 (pmm) cc_final: 0.3908 (pmm) REVERT: B 133 PHE cc_start: 0.8696 (t80) cc_final: 0.8354 (t80) REVERT: B 146 MET cc_start: 0.9054 (mmm) cc_final: 0.8209 (mmm) REVERT: B 157 LYS cc_start: 0.9375 (mttt) cc_final: 0.9046 (tptt) REVERT: B 187 MET cc_start: 0.6837 (ttm) cc_final: 0.6297 (ttm) REVERT: B 195 ASN cc_start: 0.8595 (m110) cc_final: 0.8150 (m-40) REVERT: B 209 PHE cc_start: 0.8537 (p90) cc_final: 0.8197 (p90) REVERT: B 233 GLU cc_start: 0.7459 (pp20) cc_final: 0.6689 (pp20) REVERT: B 249 MET cc_start: 0.9244 (tmm) cc_final: 0.8933 (tmm) REVERT: B 319 ASN cc_start: 0.9051 (t0) cc_final: 0.8438 (t0) REVERT: B 334 PHE cc_start: 0.9219 (t80) cc_final: 0.8948 (t80) REVERT: B 341 CYS cc_start: 0.8601 (m) cc_final: 0.8255 (m) REVERT: C 111 ASN cc_start: 0.8661 (t0) cc_final: 0.8334 (t0) REVERT: C 179 TYR cc_start: 0.9215 (t80) cc_final: 0.8961 (t80) REVERT: C 207 ASN cc_start: 0.9001 (p0) cc_final: 0.8543 (p0) REVERT: C 218 MET cc_start: 0.9271 (mmm) cc_final: 0.8617 (mmm) REVERT: C 228 TRP cc_start: 0.8816 (m-10) cc_final: 0.8354 (m-90) REVERT: D 59 TRP cc_start: 0.9266 (t60) cc_final: 0.8880 (t60) REVERT: D 224 ASN cc_start: 0.8975 (m-40) cc_final: 0.8669 (m-40) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1903 time to fit residues: 56.7620 Evaluate side-chains 162 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 0.0370 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079339 restraints weight = 23119.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.080516 restraints weight = 13681.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.081991 restraints weight = 10538.888| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9010 Z= 0.167 Angle : 0.628 10.169 12157 Z= 0.316 Chirality : 0.041 0.168 1334 Planarity : 0.004 0.043 1548 Dihedral : 6.043 114.615 1232 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.50 (0.26), residues: 1077 helix: 1.51 (0.22), residues: 597 sheet: -0.75 (0.67), residues: 48 loop : -1.25 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 374 HIS 0.007 0.001 HIS D 164 PHE 0.032 0.002 PHE C 174 TYR 0.039 0.002 TYR C 178 ARG 0.004 0.000 ARG C 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.68 seconds wall clock time: 38 minutes 52.08 seconds (2332.08 seconds total)