Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 03:49:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/10_2023/7ns4_12560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/10_2023/7ns4_12560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/10_2023/7ns4_12560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/10_2023/7ns4_12560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/10_2023/7ns4_12560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/10_2023/7ns4_12560.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 25 5.16 5 C 3534 2.51 5 N 924 2.21 5 O 980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 9": "OE1" <-> "OE2" Residue "b GLU 79": "OE1" <-> "OE2" Residue "b TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 133": "OE1" <-> "OE2" Residue "b TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 13": "OD1" <-> "OD2" Residue "i ARG 33": "NH1" <-> "NH2" Residue "i PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 101": "NH1" <-> "NH2" Residue "i ARG 105": "NH1" <-> "NH2" Residue "i PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 190": "OE1" <-> "OE2" Residue "i ARG 355": "NH1" <-> "NH2" Residue "i PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 507": "OE1" <-> "OE2" Residue "i TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 5465 Number of models: 1 Model: "" Number of chains: 4 Chain: "b" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2649 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 5 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 88 Chain: "i" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2814 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 14, 'TRANS': 343} Chain breaks: 5 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2349 SG CYS b 379 57.902 85.341 19.708 1.00 52.55 S ATOM 2524 SG CYS b 401 54.671 86.716 21.660 1.00 47.36 S ATOM 2530 SG CYS b 404 58.085 87.851 22.564 1.00 70.82 S ATOM 4696 SG CYS i 395 49.363 58.083 32.758 1.00 31.89 S ATOM 4844 SG CYS i 434 52.288 56.532 35.017 1.00 21.26 S ATOM 4864 SG CYS i 437 51.293 54.917 31.840 1.00 20.06 S Time building chain proxies: 3.40, per 1000 atoms: 0.62 Number of scatterers: 5465 At special positions: 0 Unit cell: (97.96, 99.54, 129.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 25 16.00 O 980 8.00 N 924 7.00 C 3534 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: 1.99 Conformation dependent library (CDL) restraints added in 721.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 381 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 404 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 379 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 401 " pdb=" ZN i 601 " pdb="ZN ZN i 601 " - pdb=" NE2 HIS b 356 " pdb="ZN ZN i 601 " - pdb=" SG CYS i 434 " pdb="ZN ZN i 601 " - pdb=" SG CYS i 395 " pdb="ZN ZN i 601 " - pdb=" SG CYS i 437 " Number of angles added : 6 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 59.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'b' and resid 3 through 15 removed outlier: 3.697A pdb=" N GLU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS b 14 " --> pdb=" O THR b 10 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE b 15 " --> pdb=" O GLU b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 54 removed outlier: 4.353A pdb=" N CYS b 29 " --> pdb=" O ASN b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 113 removed outlier: 4.826A pdb=" N GLU b 79 " --> pdb=" O GLU b 75 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN b 107 " --> pdb=" O SER b 103 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS b 108 " --> pdb=" O ASN b 104 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER b 109 " --> pdb=" O ARG b 105 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASN b 112 " --> pdb=" O LYS b 108 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS b 113 " --> pdb=" O SER b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 119 through 122 No H-bonds generated for 'chain 'b' and resid 119 through 122' Processing helix chain 'b' and resid 134 through 146 removed outlier: 3.632A pdb=" N GLY b 140 " --> pdb=" O ASN b 136 " (cutoff:3.500A) Processing helix chain 'b' and resid 157 through 166 removed outlier: 4.495A pdb=" N GLN b 161 " --> pdb=" O ASN b 157 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR b 162 " --> pdb=" O GLU b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 188 removed outlier: 4.679A pdb=" N GLU b 176 " --> pdb=" O LYS b 172 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE b 177 " --> pdb=" O GLU b 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 193 through 201 removed outlier: 4.504A pdb=" N LYS b 197 " --> pdb=" O GLU b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 210 through 223 Processing helix chain 'b' and resid 285 through 300 removed outlier: 4.253A pdb=" N SER b 290 " --> pdb=" O LYS b 286 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU b 291 " --> pdb=" O GLU b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 329 removed outlier: 3.765A pdb=" N PHE b 319 " --> pdb=" O GLY b 315 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLN b 320 " --> pdb=" O LEU b 316 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE b 321 " --> pdb=" O ILE b 317 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 354 Processing helix chain 'b' and resid 386 through 392 Processing helix chain 'i' and resid 12 through 19 removed outlier: 3.812A pdb=" N LEU i 16 " --> pdb=" O VAL i 12 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS i 17 " --> pdb=" O ASP i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 59 removed outlier: 3.835A pdb=" N LEU i 29 " --> pdb=" O ILE i 25 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG i 33 " --> pdb=" O LEU i 29 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE i 34 " --> pdb=" O LEU i 30 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA i 39 " --> pdb=" O LYS i 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE i 41 " --> pdb=" O THR i 37 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER i 47 " --> pdb=" O LYS i 43 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA i 54 " --> pdb=" O GLU i 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU i 55 " --> pdb=" O HIS i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 117 removed outlier: 4.237A pdb=" N ALA i 72 " --> pdb=" O GLU i 68 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS i 83 " --> pdb=" O ARG i 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE i 84 " --> pdb=" O LYS i 80 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN i 97 " --> pdb=" O LYS i 93 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG i 105 " --> pdb=" O ARG i 101 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE i 109 " --> pdb=" O ARG i 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU i 112 " --> pdb=" O PHE i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 153 removed outlier: 4.122A pdb=" N TRP i 138 " --> pdb=" O LYS i 134 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU i 146 " --> pdb=" O TYR i 142 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP i 149 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG i 153 " --> pdb=" O ASP i 149 " (cutoff:3.500A) Processing helix chain 'i' and resid 169 through 177 Processing helix chain 'i' and resid 186 through 199 removed outlier: 3.957A pdb=" N LEU i 199 " --> pdb=" O SER i 195 " (cutoff:3.500A) Processing helix chain 'i' and resid 207 through 213 removed outlier: 4.168A pdb=" N GLU i 213 " --> pdb=" O SER i 209 " (cutoff:3.500A) Processing helix chain 'i' and resid 215 through 221 removed outlier: 3.943A pdb=" N THR i 219 " --> pdb=" O LYS i 215 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS i 220 " --> pdb=" O LYS i 216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS i 221 " --> pdb=" O THR i 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 215 through 221' Processing helix chain 'i' and resid 226 through 235 Processing helix chain 'i' and resid 354 through 371 Processing helix chain 'i' and resid 378 through 389 removed outlier: 4.253A pdb=" N SER i 388 " --> pdb=" O SER i 384 " (cutoff:3.500A) Processing helix chain 'i' and resid 421 through 428 Processing helix chain 'i' and resid 441 through 446 Processing helix chain 'i' and resid 474 through 485 Processing sheet with id=AA1, first strand: chain 'i' and resid 509 through 514 removed outlier: 3.924A pdb=" N MET i 513 " --> pdb=" O PRO i 462 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE i 463 " --> pdb=" O TYR i 471 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU i 465 " --> pdb=" O ASN i 469 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN i 469 " --> pdb=" O LEU i 465 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL b 416 " --> pdb=" O PRO b 374 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU b 377 " --> pdb=" O HIS b 381 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N HIS b 381 " --> pdb=" O LEU b 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'i' and resid 495 through 498 removed outlier: 3.549A pdb=" N LYS i 503 " --> pdb=" O ASP i 498 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 819 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: 1.32 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1713 1.35 - 1.47: 1354 1.47 - 1.59: 2473 1.59 - 1.72: 0 1.72 - 1.84: 36 Bond restraints: 5576 Sorted by residual: bond pdb=" CG1 ILE b 311 " pdb=" CD1 ILE b 311 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.03e+00 bond pdb=" CB LEU i 146 " pdb=" CG LEU i 146 " ideal model delta sigma weight residual 1.530 1.506 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" CB THR i 392 " pdb=" CG2 THR i 392 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CA THR i 152 " pdb=" C THR i 152 " ideal model delta sigma weight residual 1.518 1.470 0.048 4.01e-02 6.22e+02 1.44e+00 bond pdb=" CG LEU i 385 " pdb=" CD1 LEU i 385 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 ... (remaining 5571 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.69: 137 106.69 - 113.53: 3216 113.53 - 120.36: 2116 120.36 - 127.20: 2025 127.20 - 134.03: 56 Bond angle restraints: 7550 Sorted by residual: angle pdb=" CA GLN b 85 " pdb=" CB GLN b 85 " pdb=" CG GLN b 85 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.76e+00 angle pdb=" C PRO b 343 " pdb=" N PHE b 344 " pdb=" CA PHE b 344 " ideal model delta sigma weight residual 123.91 128.99 -5.08 1.66e+00 3.63e-01 9.36e+00 angle pdb=" CG1 ILE i 454 " pdb=" CB ILE i 454 " pdb=" CG2 ILE i 454 " ideal model delta sigma weight residual 110.70 101.85 8.85 3.00e+00 1.11e-01 8.70e+00 angle pdb=" CA PRO i 449 " pdb=" C PRO i 449 " pdb=" N PHE i 450 " ideal model delta sigma weight residual 114.75 118.95 -4.20 1.45e+00 4.76e-01 8.38e+00 angle pdb=" CA LEU i 205 " pdb=" CB LEU i 205 " pdb=" CG LEU i 205 " ideal model delta sigma weight residual 116.30 126.17 -9.87 3.50e+00 8.16e-02 7.95e+00 ... (remaining 7545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3010 17.43 - 34.85: 285 34.85 - 52.28: 54 52.28 - 69.70: 9 69.70 - 87.13: 4 Dihedral angle restraints: 3362 sinusoidal: 1285 harmonic: 2077 Sorted by residual: dihedral pdb=" CA PHE b 344 " pdb=" C PHE b 344 " pdb=" N ASP b 345 " pdb=" CA ASP b 345 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA SER i 374 " pdb=" C SER i 374 " pdb=" N GLN i 375 " pdb=" CA GLN i 375 " ideal model delta harmonic sigma weight residual 180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LEU b 21 " pdb=" C LEU b 21 " pdb=" N GLU b 22 " pdb=" CA GLU b 22 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 3359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 670 0.051 - 0.103: 185 0.103 - 0.154: 27 0.154 - 0.205: 3 0.205 - 0.256: 3 Chirality restraints: 888 Sorted by residual: chirality pdb=" CG LEU b 21 " pdb=" CB LEU b 21 " pdb=" CD1 LEU b 21 " pdb=" CD2 LEU b 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE b 344 " pdb=" N PHE b 344 " pdb=" C PHE b 344 " pdb=" CB PHE b 344 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE i 454 " pdb=" CA ILE i 454 " pdb=" CG1 ILE i 454 " pdb=" CG2 ILE i 454 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 885 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET b 151 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO b 152 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO b 152 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO b 152 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 302 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ILE b 302 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE b 302 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE b 303 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE i 25 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO i 26 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO i 26 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO i 26 " -0.020 5.00e-02 4.00e+02 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 95 2.67 - 3.23: 5503 3.23 - 3.79: 7874 3.79 - 4.34: 9977 4.34 - 4.90: 16438 Nonbonded interactions: 39887 Sorted by model distance: nonbonded pdb=" N SER b 2 " pdb=" OD1 ASP i 13 " model vdw 2.116 2.520 nonbonded pdb=" O PHE i 7 " pdb=" OD1 ASN i 8 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR i 471 " pdb=" OD1 ASP i 498 " model vdw 2.194 2.440 nonbonded pdb=" ND2 ASN i 467 " pdb=" OD2 ASP i 498 " model vdw 2.209 2.520 nonbonded pdb=" O LEU i 22 " pdb=" NH1 ARG i 105 " model vdw 2.212 2.520 ... (remaining 39882 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: 1.010 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: 4.940 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.260 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.006 0.056 5576 Z= 0.394 Angle : 0.795 9.870 7550 Z= 0.409 Chirality : 0.048 0.256 888 Planarity : 0.004 0.051 936 Dihedral : 14.398 87.130 1994 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -1.02 (0.34), residues: 674 helix: 0.47 (0.26), residues: 433 sheet: -2.03 (1.80), residues: 10 loop : -2.89 (0.41), residues: 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.687 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1990 time to fit residues: 19.8171 Evaluate side-chains 61 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.668 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 32 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 0.0870 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 8 ASN ** i 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5576 Z= 0.199 Angle : 0.612 8.343 7550 Z= 0.310 Chirality : 0.040 0.185 888 Planarity : 0.004 0.037 936 Dihedral : 5.062 23.833 726 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 1.19 % Allowed : 9.01 % Favored : 89.80 % 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: -0.40 (0.35), residues: 674 helix: 0.99 (0.27), residues: 419 sheet: None (None), residues: 0 loop : -2.51 (0.40), residues: 255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.670 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.2027 time to fit residues: 20.3924 Evaluate side-chains 69 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0553 time to fit residues: 1.4081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 52 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 47 optimal weight: 0.0030 overall best weight: 0.2288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 201 ASN ** i 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5576 Z= 0.163 Angle : 0.557 9.751 7550 Z= 0.283 Chirality : 0.039 0.180 888 Planarity : 0.003 0.037 936 Dihedral : 4.662 23.390 726 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.04 % Allowed : 11.56 % Favored : 86.39 % 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: -0.00 (0.35), residues: 674 helix: 1.34 (0.27), residues: 418 sheet: None (None), residues: 0 loop : -2.41 (0.41), residues: 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.662 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 85 average time/residue: 0.2068 time to fit residues: 22.3413 Evaluate side-chains 72 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0608 time to fit residues: 1.5517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5576 Z= 0.224 Angle : 0.610 9.189 7550 Z= 0.304 Chirality : 0.040 0.187 888 Planarity : 0.003 0.035 936 Dihedral : 4.745 22.880 726 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.19 % Allowed : 16.16 % Favored : 82.65 % 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: 0.01 (0.35), residues: 674 helix: 1.36 (0.27), residues: 419 sheet: None (None), residues: 0 loop : -2.42 (0.41), residues: 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.655 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.1790 time to fit residues: 17.8934 Evaluate side-chains 70 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0649 time to fit residues: 1.5168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 59 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 201 ASN ** i 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5576 Z= 0.141 Angle : 0.555 8.865 7550 Z= 0.276 Chirality : 0.038 0.178 888 Planarity : 0.003 0.035 936 Dihedral : 4.350 22.154 726 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.68 % Allowed : 17.69 % Favored : 81.63 % 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: 0.30 (0.35), residues: 674 helix: 1.58 (0.27), residues: 423 sheet: None (None), residues: 0 loop : -2.36 (0.41), residues: 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.683 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 79 average time/residue: 0.2087 time to fit residues: 21.1672 Evaluate side-chains 67 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0676 time to fit residues: 1.0917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.0970 chunk 16 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.0010 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 64 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5576 Z= 0.138 Angle : 0.547 8.119 7550 Z= 0.272 Chirality : 0.038 0.177 888 Planarity : 0.003 0.036 936 Dihedral : 4.191 21.348 726 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.53 % Allowed : 18.20 % Favored : 80.27 % 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: 0.49 (0.35), residues: 674 helix: 1.75 (0.27), residues: 422 sheet: None (None), residues: 0 loop : -2.32 (0.41), residues: 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.662 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 79 average time/residue: 0.1945 time to fit residues: 19.9851 Evaluate side-chains 70 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0491 time to fit residues: 0.9769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5576 Z= 0.276 Angle : 0.630 8.929 7550 Z= 0.315 Chirality : 0.041 0.188 888 Planarity : 0.004 0.036 936 Dihedral : 4.560 21.779 726 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.53 % Allowed : 19.22 % Favored : 79.25 % 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: 0.32 (0.35), residues: 674 helix: 1.65 (0.27), residues: 418 sheet: None (None), residues: 0 loop : -2.39 (0.41), residues: 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.721 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.1789 time to fit residues: 17.4029 Evaluate side-chains 72 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1261 time to fit residues: 1.8234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 chunk 45 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 overall best weight: 0.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5576 Z= 0.158 Angle : 0.578 8.575 7550 Z= 0.289 Chirality : 0.039 0.181 888 Planarity : 0.003 0.036 936 Dihedral : 4.311 21.348 726 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % 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 (0.35), residues: 674 helix: 1.70 (0.27), residues: 424 sheet: None (None), residues: 0 loop : -2.39 (0.41), residues: 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.686 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2162 time to fit residues: 19.6121 Evaluate side-chains 66 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5576 Z= 0.196 Angle : 0.601 8.615 7550 Z= 0.302 Chirality : 0.039 0.183 888 Planarity : 0.004 0.036 936 Dihedral : 4.418 21.336 726 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.02 % Allowed : 20.75 % Favored : 78.23 % 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: 0.42 (0.35), residues: 674 helix: 1.71 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -2.39 (0.42), residues: 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.607 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.1802 time to fit residues: 16.4759 Evaluate side-chains 69 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0582 time to fit residues: 1.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 0.0270 chunk 54 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 33 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5576 Z= 0.177 Angle : 0.588 8.469 7550 Z= 0.294 Chirality : 0.039 0.181 888 Planarity : 0.004 0.038 936 Dihedral : 4.359 21.265 726 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.68 % Allowed : 21.09 % Favored : 78.23 % 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: 0.54 (0.35), residues: 674 helix: 1.80 (0.27), residues: 424 sheet: None (None), residues: 0 loop : -2.34 (0.42), residues: 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.667 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 70 average time/residue: 0.1860 time to fit residues: 17.2000 Evaluate side-chains 66 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 62 optimal weight: 0.0470 chunk 36 optimal weight: 0.6980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107168 restraints weight = 9009.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108815 restraints weight = 6020.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110030 restraints weight = 4499.763| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5576 Z= 0.187 Angle : 0.601 9.162 7550 Z= 0.298 Chirality : 0.039 0.182 888 Planarity : 0.004 0.039 936 Dihedral : 4.370 21.366 726 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.51 % Allowed : 22.11 % Favored : 77.38 % 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: 0.54 (0.35), residues: 674 helix: 1.80 (0.27), residues: 424 sheet: None (None), residues: 0 loop : -2.34 (0.42), residues: 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1337.93 seconds wall clock time: 24 minutes 57.40 seconds (1497.40 seconds total)