Starting phenix.real_space_refine on Mon Sep 23 21:14:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/09_2024/7ns4_12560.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/09_2024/7ns4_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_12560/09_2024/7ns4_12560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/09_2024/7ns4_12560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/09_2024/7ns4_12560.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns4_12560/09_2024/7ns4_12560.cif" } 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. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.84, per 1000 atoms: 0.70 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 - 3.00 Amino acid : True - 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: 1.28 Conformation dependent library (CDL) restraints added in 605.8 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: 0.46 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: 1.26 Time building geometry restraints manager: 1.51 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: 0.00 - 1.97: 7312 1.97 - 3.95: 197 3.95 - 5.92: 30 5.92 - 7.90: 7 7.90 - 9.87: 4 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 3.120 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 3.040 nonbonded pdb=" ND2 ASN i 467 " pdb=" OD2 ASP i 498 " model vdw 2.209 3.120 nonbonded pdb=" O LEU i 22 " pdb=" NH1 ARG i 105 " model vdw 2.212 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.810 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP i 356 HIS 0.008 0.001 HIS b 356 PHE 0.017 0.002 PHE b 303 TYR 0.015 0.002 TYR i 95 ARG 0.006 0.001 ARG b 86 *********************** 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 : 0.611 Fit side-chains REVERT: i 361 ASP cc_start: 0.7924 (t0) cc_final: 0.7649 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1887 time to fit residues: 18.6853 Evaluate side-chains 61 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 0.0870 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 32 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 overall best weight: 0.1734 ------------------------------------------------------------------------------- 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: 0.8125 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5576 Z= 0.162 Angle : 0.598 8.258 7550 Z= 0.305 Chirality : 0.040 0.180 888 Planarity : 0.004 0.039 936 Dihedral : 4.845 23.258 726 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.19 % Allowed : 7.99 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.35), residues: 674 helix: 1.03 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -2.51 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP i 356 HIS 0.004 0.001 HIS b 354 PHE 0.015 0.001 PHE b 303 TYR 0.012 0.001 TYR i 185 ARG 0.004 0.000 ARG b 86 *********************** 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 86 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.640 Fit side-chains REVERT: b 11 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7459 (mt-10) REVERT: b 320 GLN cc_start: 0.8053 (tp40) cc_final: 0.7637 (tp40) REVERT: i 361 ASP cc_start: 0.7825 (t0) cc_final: 0.7445 (t0) outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.1763 time to fit residues: 19.8544 Evaluate side-chains 68 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 328 ILE Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 454 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 52 optimal weight: 0.0050 chunk 42 optimal weight: 0.2980 chunk 17 optimal weight: 0.0770 chunk 62 optimal weight: 0.0570 chunk 67 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 47 optimal weight: 0.1980 overall best weight: 0.0870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 201 ASN i 97 GLN ** i 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5576 Z= 0.138 Angle : 0.551 9.125 7550 Z= 0.281 Chirality : 0.038 0.175 888 Planarity : 0.003 0.038 936 Dihedral : 4.438 22.741 726 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.55 % Allowed : 11.39 % Favored : 86.05 % 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: 0.05 (0.35), residues: 674 helix: 1.33 (0.27), residues: 424 sheet: None (None), residues: 0 loop : -2.36 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP i 356 HIS 0.003 0.001 HIS b 354 PHE 0.012 0.001 PHE b 351 TYR 0.012 0.001 TYR i 185 ARG 0.004 0.000 ARG b 86 *********************** 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 100 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.650 Fit side-chains REVERT: b 11 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7415 (mt-10) REVERT: b 319 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8681 (m-10) REVERT: b 320 GLN cc_start: 0.8144 (tp40) cc_final: 0.7591 (tp40) REVERT: i 68 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7165 (tm-30) REVERT: i 190 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7734 (tm-30) REVERT: i 361 ASP cc_start: 0.7767 (t0) cc_final: 0.7421 (t0) outliers start: 15 outliers final: 6 residues processed: 95 average time/residue: 0.2001 time to fit residues: 24.1095 Evaluate side-chains 79 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 8 ASN Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 205 LEU Chi-restraints excluded: chain i residue 454 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 17 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5576 Z= 0.214 Angle : 0.606 8.519 7550 Z= 0.306 Chirality : 0.041 0.253 888 Planarity : 0.004 0.037 936 Dihedral : 4.565 22.240 726 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.55 % Allowed : 13.61 % Favored : 83.84 % 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: 0.13 (0.35), residues: 674 helix: 1.42 (0.27), residues: 420 sheet: None (None), residues: 0 loop : -2.34 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP i 356 HIS 0.003 0.001 HIS b 354 PHE 0.012 0.001 PHE b 344 TYR 0.013 0.001 TYR i 95 ARG 0.006 0.001 ARG i 355 *********************** 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 83 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.651 Fit side-chains REVERT: b 11 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7440 (mt-10) REVERT: b 47 LEU cc_start: 0.9081 (tp) cc_final: 0.8812 (tt) REVERT: b 319 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8705 (m-10) REVERT: b 320 GLN cc_start: 0.8281 (tp40) cc_final: 0.7812 (tp40) REVERT: i 68 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7302 (tm-30) outliers start: 15 outliers final: 7 residues processed: 77 average time/residue: 0.1729 time to fit residues: 17.3174 Evaluate side-chains 73 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 502 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 46 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 60 optimal weight: 0.0060 chunk 13 optimal weight: 0.5980 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.1877 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= 0.161 Angle : 0.563 7.517 7550 Z= 0.286 Chirality : 0.039 0.180 888 Planarity : 0.003 0.039 936 Dihedral : 4.386 22.090 726 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.89 % Allowed : 15.48 % 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: 0.19 (0.35), residues: 674 helix: 1.44 (0.27), residues: 425 sheet: None (None), residues: 0 loop : -2.31 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP i 356 HIS 0.004 0.001 HIS b 354 PHE 0.011 0.001 PHE b 351 TYR 0.011 0.001 TYR i 185 ARG 0.004 0.000 ARG i 355 *********************** 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 88 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.597 Fit side-chains REVERT: b 11 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7415 (mt-10) REVERT: b 47 LEU cc_start: 0.9060 (tp) cc_final: 0.8796 (tt) REVERT: b 319 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8682 (m-10) REVERT: b 320 GLN cc_start: 0.8283 (tp40) cc_final: 0.7779 (tp40) REVERT: i 9 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: i 68 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7276 (tm-30) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.1709 time to fit residues: 18.3453 Evaluate side-chains 77 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 9 GLU Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 207 LEU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 502 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 35 optimal weight: 0.1980 chunk 64 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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: 0.8149 moved from start: 0.1764 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= 0.216 Angle : 0.597 7.246 7550 Z= 0.305 Chirality : 0.040 0.183 888 Planarity : 0.004 0.040 936 Dihedral : 4.531 21.928 726 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.06 % Allowed : 17.01 % Favored : 79.93 % 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 (0.35), residues: 674 helix: 1.34 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -2.37 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP i 356 HIS 0.004 0.001 HIS b 354 PHE 0.013 0.001 PHE b 344 TYR 0.014 0.001 TYR i 95 ARG 0.003 0.000 ARG i 86 *********************** 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 81 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.589 Fit side-chains REVERT: b 11 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7435 (mt-10) REVERT: b 47 LEU cc_start: 0.9137 (tp) cc_final: 0.8894 (tt) REVERT: b 319 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8677 (m-10) REVERT: b 320 GLN cc_start: 0.8519 (tp40) cc_final: 0.8118 (tp40) REVERT: i 68 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7121 (tm-30) REVERT: i 471 TYR cc_start: 0.6529 (m-80) cc_final: 0.6222 (m-80) outliers start: 18 outliers final: 14 residues processed: 77 average time/residue: 0.1715 time to fit residues: 17.4838 Evaluate side-chains 74 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 115 LYS Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 220 LEU Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 328 ILE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 207 LEU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 502 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5576 Z= 0.321 Angle : 0.663 7.389 7550 Z= 0.339 Chirality : 0.043 0.191 888 Planarity : 0.004 0.044 936 Dihedral : 4.911 22.532 726 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.74 % Allowed : 16.50 % Favored : 79.76 % 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: -0.14 (0.35), residues: 674 helix: 1.17 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -2.45 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP i 356 HIS 0.006 0.001 HIS b 354 PHE 0.016 0.002 PHE b 344 TYR 0.015 0.002 TYR i 185 ARG 0.003 0.000 ARG i 355 *********************** 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 84 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.714 Fit side-chains REVERT: b 87 GLN cc_start: 0.7964 (mm110) cc_final: 0.7588 (tp40) REVERT: b 319 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8652 (m-10) REVERT: b 320 GLN cc_start: 0.8562 (tp40) cc_final: 0.8207 (tp40) REVERT: i 68 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7243 (tm-30) REVERT: i 471 TYR cc_start: 0.6945 (m-80) cc_final: 0.6700 (m-80) outliers start: 22 outliers final: 17 residues processed: 79 average time/residue: 0.1798 time to fit residues: 18.7286 Evaluate side-chains 77 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 115 LYS Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 220 LEU Chi-restraints excluded: chain b residue 302 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 328 ILE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 205 LEU Chi-restraints excluded: chain i residue 207 LEU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 502 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 0.2980 chunk 60 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 61 optimal weight: 0.0020 chunk 37 optimal weight: 0.5980 overall best weight: 0.2192 ------------------------------------------------------------------------------- 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: 0.8128 moved from start: 0.1852 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= 0.166 Angle : 0.583 10.788 7550 Z= 0.294 Chirality : 0.039 0.184 888 Planarity : 0.003 0.043 936 Dihedral : 4.477 21.878 726 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.23 % Allowed : 17.35 % Favored : 79.42 % 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: 0.17 (0.35), residues: 674 helix: 1.45 (0.27), residues: 424 sheet: None (None), residues: 0 loop : -2.36 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP i 356 HIS 0.002 0.001 HIS b 32 PHE 0.011 0.001 PHE b 344 TYR 0.011 0.001 TYR i 185 ARG 0.004 0.000 ARG i 86 *********************** 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 86 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.620 Fit side-chains REVERT: b 11 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7453 (mt-10) REVERT: b 151 MET cc_start: 0.8631 (ptp) cc_final: 0.8302 (ptt) REVERT: b 319 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8695 (m-10) REVERT: b 320 GLN cc_start: 0.8490 (tp40) cc_final: 0.8094 (tp40) REVERT: i 68 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7123 (tm-30) REVERT: i 382 TYR cc_start: 0.9228 (m-80) cc_final: 0.8959 (m-80) REVERT: i 471 TYR cc_start: 0.6650 (m-80) cc_final: 0.6335 (m-80) outliers start: 19 outliers final: 12 residues processed: 81 average time/residue: 0.1656 time to fit residues: 17.8933 Evaluate side-chains 73 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 220 LEU Chi-restraints excluded: chain b residue 302 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 502 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.0000 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.0010 overall best weight: 0.3768 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5576 Z= 0.217 Angle : 0.616 10.087 7550 Z= 0.310 Chirality : 0.041 0.184 888 Planarity : 0.004 0.043 936 Dihedral : 4.586 21.642 726 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.06 % Allowed : 17.69 % 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: 0.05 (0.35), residues: 674 helix: 1.32 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -2.46 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP i 356 HIS 0.003 0.001 HIS b 356 PHE 0.013 0.001 PHE b 344 TYR 0.013 0.001 TYR i 185 ARG 0.003 0.000 ARG i 86 *********************** 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 77 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.625 Fit side-chains REVERT: b 151 MET cc_start: 0.8649 (ptp) cc_final: 0.8442 (ptm) REVERT: b 319 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8680 (m-10) REVERT: b 320 GLN cc_start: 0.8529 (tp40) cc_final: 0.8167 (tp40) REVERT: i 68 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7121 (tm-30) REVERT: i 382 TYR cc_start: 0.9232 (m-80) cc_final: 0.8915 (m-80) REVERT: i 471 TYR cc_start: 0.6759 (m-80) cc_final: 0.6450 (m-80) outliers start: 18 outliers final: 15 residues processed: 72 average time/residue: 0.1751 time to fit residues: 16.7497 Evaluate side-chains 75 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 115 LYS Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 220 LEU Chi-restraints excluded: chain b residue 302 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 207 LEU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 502 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.0070 chunk 63 optimal weight: 0.2980 chunk 54 optimal weight: 0.4980 chunk 5 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5576 Z= 0.172 Angle : 0.585 9.675 7550 Z= 0.294 Chirality : 0.040 0.183 888 Planarity : 0.004 0.043 936 Dihedral : 4.403 21.141 726 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.72 % Allowed : 18.03 % 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: 0.28 (0.35), residues: 674 helix: 1.57 (0.26), residues: 423 sheet: None (None), residues: 0 loop : -2.37 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP i 356 HIS 0.002 0.001 HIS b 356 PHE 0.011 0.001 PHE b 351 TYR 0.014 0.001 TYR i 95 ARG 0.004 0.000 ARG i 86 ********************** 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 81 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.633 Fit side-chains REVERT: b 11 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7479 (mt-10) REVERT: b 319 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: b 320 GLN cc_start: 0.8509 (tp40) cc_final: 0.8127 (tp40) REVERT: i 68 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7063 (tm-30) REVERT: i 382 TYR cc_start: 0.9251 (m-80) cc_final: 0.8924 (m-80) REVERT: i 471 TYR cc_start: 0.6669 (m-80) cc_final: 0.6342 (m-80) outliers start: 16 outliers final: 12 residues processed: 77 average time/residue: 0.1781 time to fit residues: 18.2397 Evaluate side-chains 72 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 220 LEU Chi-restraints excluded: chain b residue 302 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 502 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.0170 chunk 54 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104815 restraints weight = 9063.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106488 restraints weight = 6082.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107695 restraints weight = 4594.455| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5576 Z= 0.221 Angle : 0.615 9.190 7550 Z= 0.311 Chirality : 0.041 0.185 888 Planarity : 0.004 0.043 936 Dihedral : 4.535 20.867 726 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.55 % Allowed : 18.20 % 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: 0.20 (0.35), residues: 674 helix: 1.49 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -2.40 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP i 356 HIS 0.003 0.001 HIS b 356 PHE 0.013 0.001 PHE i 87 TYR 0.015 0.001 TYR i 95 ARG 0.004 0.000 ARG i 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1319.64 seconds wall clock time: 24 minutes 30.17 seconds (1470.17 seconds total)