Starting phenix.real_space_refine on Sun Nov 17 13:32:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqg_35661/11_2024/8iqg_35661.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqg_35661/11_2024/8iqg_35661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqg_35661/11_2024/8iqg_35661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqg_35661/11_2024/8iqg_35661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqg_35661/11_2024/8iqg_35661.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqg_35661/11_2024/8iqg_35661.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6634 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5428 2.51 5 N 1537 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8517 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1439 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 210 Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 612 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2950 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 22, 'TRANS': 378} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 19, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 173 Chain: "B" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2683 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 349} Chain breaks: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 6, 'ARG:plan': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 5.52, per 1000 atoms: 0.65 Number of scatterers: 8517 At special positions: 0 Unit cell: (79, 89, 127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1520 8.00 N 1537 7.00 C 5428 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: 2.40 Conformation dependent library (CDL) restraints added in 969.2 milliseconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 20 sheets defined 20.1% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 490 through 502 removed outlier: 3.565A pdb=" N GLN A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 removed outlier: 3.664A pdb=" N ASP A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 652 through 675 Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.660A pdb=" N PHE D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 114 Processing helix chain 'D' and resid 120 through 131 Processing helix chain 'E' and resid 25 through 29 removed outlier: 4.304A pdb=" N ILE E 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 50 through 75 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'C' and resid 12 through 32 Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.352A pdb=" N TYR C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 572 removed outlier: 3.521A pdb=" N ASP C 379 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 686 removed outlier: 4.084A pdb=" N TYR B 340 " --> pdb=" O ILE A 686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 54 removed outlier: 6.508A pdb=" N ASP C 52 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG C 65 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 83 removed outlier: 7.356A pdb=" N ASN C 77 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN C 122 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 79 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS C 120 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 81 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'C' and resid 172 through 173 removed outlier: 6.833A pdb=" N ARG C 172 " --> pdb=" O VAL C 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 182 through 185 removed outlier: 3.855A pdb=" N GLY C 182 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 230 through 235 removed outlier: 6.886A pdb=" N VAL C 246 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL C 233 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY C 244 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TRP C 235 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU C 242 " --> pdb=" O TRP C 235 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 247 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS C 267 " --> pdb=" O ILE C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 279 through 281 removed outlier: 3.834A pdb=" N HIS C 311 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 320 through 323 removed outlier: 6.766A pdb=" N SER C 336 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.402A pdb=" N CYS B 370 " --> pdb=" O CYS B 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 16 through 18 removed outlier: 6.789A pdb=" N ALA B 35 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.673A pdb=" N VAL B 41 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN B 61 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 43 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 71 removed outlier: 5.191A pdb=" N VAL B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 90 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 124 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 92 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 120 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.468A pdb=" N ALA B 147 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 135 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA B 145 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 154 through 156 removed outlier: 6.847A pdb=" N ILE B 155 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 174 through 177 removed outlier: 3.697A pdb=" N PHE B 207 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N SER B 199 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL B 205 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 241 through 242 removed outlier: 3.644A pdb=" N LEU B 250 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU B 250 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE B 269 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR B 267 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 279 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 288 through 293 removed outlier: 6.795A pdb=" N ALA B 322 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 291 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 320 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 299 261 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2635 1.33 - 1.45: 1322 1.45 - 1.57: 4713 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 8717 Sorted by residual: bond pdb=" CG LEU D 92 " pdb=" CD2 LEU D 92 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CB VAL C 35 " pdb=" CG2 VAL C 35 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.51e-01 bond pdb=" CG LEU C 333 " pdb=" CD1 LEU C 333 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.75e-01 bond pdb=" CG LEU B 240 " pdb=" CD2 LEU B 240 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.04e-01 bond pdb=" CA LEU C 34 " pdb=" C LEU C 34 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.47e-01 ... (remaining 8712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11721 1.95 - 3.89: 148 3.89 - 5.84: 18 5.84 - 7.78: 5 7.78 - 9.73: 1 Bond angle restraints: 11893 Sorted by residual: angle pdb=" N ASP C 33 " pdb=" CA ASP C 33 " pdb=" C ASP C 33 " ideal model delta sigma weight residual 114.56 110.23 4.33 1.27e+00 6.20e-01 1.16e+01 angle pdb=" C PRO C 387 " pdb=" N TRP C 388 " pdb=" CA TRP C 388 " ideal model delta sigma weight residual 121.54 127.08 -5.54 1.91e+00 2.74e-01 8.41e+00 angle pdb=" N GLU A 606 " pdb=" CA GLU A 606 " pdb=" C GLU A 606 " ideal model delta sigma weight residual 110.97 114.10 -3.13 1.09e+00 8.42e-01 8.26e+00 angle pdb=" N THR C 28 " pdb=" CA THR C 28 " pdb=" C THR C 28 " ideal model delta sigma weight residual 109.81 116.05 -6.24 2.21e+00 2.05e-01 7.98e+00 angle pdb=" CA LEU D 61 " pdb=" CB LEU D 61 " pdb=" CG LEU D 61 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.73e+00 ... (remaining 11888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4500 17.96 - 35.93: 487 35.93 - 53.89: 119 53.89 - 71.86: 16 71.86 - 89.82: 10 Dihedral angle restraints: 5132 sinusoidal: 1745 harmonic: 3387 Sorted by residual: dihedral pdb=" CA TRP A 604 " pdb=" C TRP A 604 " pdb=" N GLU A 605 " pdb=" CA GLU A 605 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLU A 605 " pdb=" C GLU A 605 " pdb=" N GLU A 606 " pdb=" CA GLU A 606 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CB GLU C 124 " pdb=" CG GLU C 124 " pdb=" CD GLU C 124 " pdb=" OE1 GLU C 124 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 881 0.034 - 0.069: 313 0.069 - 0.103: 104 0.103 - 0.138: 60 0.138 - 0.172: 2 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA THR C 28 " pdb=" N THR C 28 " pdb=" C THR C 28 " pdb=" CB THR C 28 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA LEU D 61 " pdb=" N LEU D 61 " pdb=" C LEU D 61 " pdb=" CB LEU D 61 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA PRO E 32 " pdb=" N PRO E 32 " pdb=" C PRO E 32 " pdb=" CB PRO E 32 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1357 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 86 " -0.027 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO C 87 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 121 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C PRO D 121 " -0.028 2.00e-02 2.50e+03 pdb=" O PRO D 121 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS D 122 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 14 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO B 15 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " -0.016 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 223 2.69 - 3.24: 8167 3.24 - 3.79: 13738 3.79 - 4.35: 17435 4.35 - 4.90: 29893 Nonbonded interactions: 69456 Sorted by model distance: nonbonded pdb=" OD1 ASP B 245 " pdb=" OH TYR B 315 " model vdw 2.133 3.040 nonbonded pdb=" OG SER B 323 " pdb=" OG SER B 326 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR E 73 " pdb=" OD2 ASP E 85 " model vdw 2.191 3.040 nonbonded pdb=" OG SER B 355 " pdb=" OD1 ASP B 357 " model vdw 2.206 3.040 nonbonded pdb=" NZ LYS E 91 " pdb=" OD2 ASP B 86 " model vdw 2.219 3.120 ... (remaining 69451 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.520 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 : 0.004 0.038 8717 Z= 0.243 Angle : 0.566 9.729 11893 Z= 0.291 Chirality : 0.044 0.172 1360 Planarity : 0.003 0.042 1536 Dihedral : 16.209 89.822 2934 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.39 % Allowed : 27.19 % Favored : 72.42 % 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: -1.06 (0.25), residues: 1150 helix: 1.54 (0.37), residues: 203 sheet: -1.84 (0.30), residues: 285 loop : -0.84 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 93 HIS 0.005 0.001 HIS C 78 PHE 0.011 0.001 PHE C 243 TYR 0.008 0.001 TYR C 409 ARG 0.005 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 189 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7636 (tp) outliers start: 3 outliers final: 0 residues processed: 188 average time/residue: 0.2443 time to fit residues: 60.1317 Evaluate side-chains 126 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 67 optimal weight: 0.0770 chunk 104 optimal weight: 9.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 65 HIS B 70 ASN ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8717 Z= 0.197 Angle : 0.622 13.114 11893 Z= 0.309 Chirality : 0.045 0.176 1360 Planarity : 0.004 0.039 1536 Dihedral : 4.387 54.076 1249 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.25 % Allowed : 27.19 % Favored : 68.56 % 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: -1.17 (0.25), residues: 1150 helix: 1.30 (0.36), residues: 218 sheet: -1.63 (0.30), residues: 298 loop : -1.05 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 179 HIS 0.005 0.001 HIS B 345 PHE 0.013 0.001 PHE D 78 TYR 0.014 0.001 TYR C 32 ARG 0.006 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 702 LYS cc_start: 0.6134 (ptmm) cc_final: 0.5035 (ptmm) REVERT: D 93 GLN cc_start: 0.7571 (tt0) cc_final: 0.7271 (tt0) REVERT: E 95 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7465 (mtp85) REVERT: C 342 LEU cc_start: 0.8952 (tp) cc_final: 0.8707 (tt) REVERT: B 18 SER cc_start: 0.8828 (t) cc_final: 0.8515 (p) REVERT: B 189 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7049 (tp) outliers start: 33 outliers final: 7 residues processed: 178 average time/residue: 0.2246 time to fit residues: 54.0334 Evaluate side-chains 138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN B 30 HIS B 70 ASN ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8717 Z= 0.216 Angle : 0.613 11.996 11893 Z= 0.301 Chirality : 0.045 0.161 1360 Planarity : 0.004 0.051 1536 Dihedral : 4.147 39.349 1249 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.87 % Allowed : 27.45 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1150 helix: 1.45 (0.36), residues: 213 sheet: -1.63 (0.30), residues: 289 loop : -1.01 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 255 HIS 0.005 0.001 HIS C 226 PHE 0.012 0.001 PHE C 61 TYR 0.010 0.001 TYR C 154 ARG 0.008 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 700 ASP cc_start: 0.6214 (p0) cc_final: 0.5961 (p0) REVERT: B 18 SER cc_start: 0.8818 (t) cc_final: 0.8576 (p) REVERT: B 297 TYR cc_start: 0.7968 (m-10) cc_final: 0.7750 (m-10) outliers start: 30 outliers final: 12 residues processed: 164 average time/residue: 0.2133 time to fit residues: 48.5423 Evaluate side-chains 135 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 70 ASN ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8717 Z= 0.227 Angle : 0.612 11.299 11893 Z= 0.300 Chirality : 0.045 0.162 1360 Planarity : 0.004 0.039 1536 Dihedral : 3.981 19.293 1247 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.71 % Allowed : 29.25 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1150 helix: 1.49 (0.36), residues: 214 sheet: -1.71 (0.27), residues: 318 loop : -0.90 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 255 HIS 0.003 0.001 HIS C 328 PHE 0.021 0.001 PHE A 508 TYR 0.009 0.001 TYR C 409 ARG 0.007 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 ASP cc_start: 0.5988 (p0) cc_final: 0.5778 (p0) REVERT: B 18 SER cc_start: 0.8754 (t) cc_final: 0.8535 (m) REVERT: B 70 ASN cc_start: 0.7657 (m110) cc_final: 0.7154 (m-40) outliers start: 21 outliers final: 16 residues processed: 147 average time/residue: 0.2215 time to fit residues: 44.8167 Evaluate side-chains 138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN B 30 HIS ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8717 Z= 0.381 Angle : 0.652 11.678 11893 Z= 0.327 Chirality : 0.046 0.180 1360 Planarity : 0.004 0.038 1536 Dihedral : 4.137 19.820 1247 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.25 % Allowed : 28.35 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1150 helix: 1.39 (0.35), residues: 220 sheet: -1.78 (0.28), residues: 308 loop : -0.96 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 93 HIS 0.011 0.001 HIS C 176 PHE 0.020 0.002 PHE A 508 TYR 0.014 0.001 TYR C 154 ARG 0.008 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 351 ASP cc_start: 0.7493 (m-30) cc_final: 0.7183 (m-30) outliers start: 33 outliers final: 22 residues processed: 139 average time/residue: 0.2237 time to fit residues: 42.5102 Evaluate side-chains 121 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.0000 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 107 optimal weight: 0.1980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 HIS B 30 HIS ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8717 Z= 0.184 Angle : 0.623 11.892 11893 Z= 0.304 Chirality : 0.046 0.215 1360 Planarity : 0.004 0.035 1536 Dihedral : 3.993 19.567 1247 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.96 % Allowed : 29.12 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1150 helix: 1.60 (0.36), residues: 214 sheet: -1.76 (0.27), residues: 324 loop : -0.86 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 255 HIS 0.019 0.001 HIS C 176 PHE 0.016 0.001 PHE A 508 TYR 0.012 0.001 TYR C 154 ARG 0.007 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 ASP cc_start: 0.5808 (p0) cc_final: 0.5550 (p0) REVERT: E 95 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7337 (mtp85) REVERT: B 351 ASP cc_start: 0.7438 (m-30) cc_final: 0.7144 (m-30) outliers start: 23 outliers final: 17 residues processed: 141 average time/residue: 0.2201 time to fit residues: 42.7682 Evaluate side-chains 130 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 50.0000 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS B 70 ASN ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8717 Z= 0.403 Angle : 0.663 10.966 11893 Z= 0.333 Chirality : 0.047 0.190 1360 Planarity : 0.004 0.077 1536 Dihedral : 4.156 19.613 1247 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.12 % Allowed : 28.22 % Favored : 67.65 % 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: -1.12 (0.24), residues: 1150 helix: 1.45 (0.36), residues: 219 sheet: -1.72 (0.28), residues: 315 loop : -0.95 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 402 HIS 0.019 0.001 HIS C 176 PHE 0.015 0.002 PHE D 78 TYR 0.014 0.002 TYR A 640 ARG 0.014 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 95 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7275 (mtp85) REVERT: B 351 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7244 (m-30) outliers start: 32 outliers final: 20 residues processed: 129 average time/residue: 0.2297 time to fit residues: 40.6568 Evaluate side-chains 123 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 351 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8717 Z= 0.215 Angle : 0.646 11.886 11893 Z= 0.316 Chirality : 0.046 0.162 1360 Planarity : 0.004 0.035 1536 Dihedral : 4.102 19.816 1247 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.74 % Allowed : 29.51 % Favored : 66.75 % 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: -1.13 (0.24), residues: 1150 helix: 1.38 (0.36), residues: 220 sheet: -1.60 (0.28), residues: 314 loop : -1.03 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 402 HIS 0.016 0.001 HIS C 176 PHE 0.013 0.001 PHE E 100 TYR 0.012 0.001 TYR C 154 ARG 0.008 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 95 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7346 (mtp85) REVERT: B 351 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7168 (m-30) outliers start: 29 outliers final: 25 residues processed: 138 average time/residue: 0.2197 time to fit residues: 41.7530 Evaluate side-chains 132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 351 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8717 Z= 0.272 Angle : 0.674 14.144 11893 Z= 0.334 Chirality : 0.046 0.215 1360 Planarity : 0.004 0.036 1536 Dihedral : 4.092 19.700 1247 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.99 % Allowed : 29.38 % Favored : 66.62 % 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: -1.06 (0.24), residues: 1150 helix: 1.45 (0.36), residues: 220 sheet: -1.51 (0.28), residues: 319 loop : -1.00 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 402 HIS 0.015 0.001 HIS C 176 PHE 0.012 0.001 PHE A 508 TYR 0.011 0.001 TYR C 154 ARG 0.012 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 GLN cc_start: 0.6339 (mp10) cc_final: 0.6044 (mp10) REVERT: E 95 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7300 (mtp85) REVERT: B 233 MET cc_start: 0.7440 (ppp) cc_final: 0.6397 (ptt) REVERT: B 351 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7209 (m-30) outliers start: 31 outliers final: 25 residues processed: 129 average time/residue: 0.2303 time to fit residues: 41.3740 Evaluate side-chains 132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 351 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8717 Z= 0.233 Angle : 0.679 13.531 11893 Z= 0.335 Chirality : 0.047 0.238 1360 Planarity : 0.004 0.035 1536 Dihedral : 4.098 20.957 1247 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.35 % Allowed : 30.03 % Favored : 66.62 % 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: -0.99 (0.24), residues: 1150 helix: 1.46 (0.36), residues: 220 sheet: -1.39 (0.28), residues: 313 loop : -1.00 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 402 HIS 0.015 0.001 HIS C 176 PHE 0.012 0.001 PHE E 100 TYR 0.011 0.001 TYR C 154 ARG 0.012 0.000 ARG E 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 95 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7264 (mtp85) REVERT: B 233 MET cc_start: 0.7373 (ppp) cc_final: 0.6414 (ptt) REVERT: B 351 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7181 (m-30) outliers start: 26 outliers final: 22 residues processed: 131 average time/residue: 0.2180 time to fit residues: 39.2248 Evaluate side-chains 132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 351 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.084996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.065548 restraints weight = 29717.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.068023 restraints weight = 16054.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069688 restraints weight = 11261.352| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8717 Z= 0.229 Angle : 0.694 13.022 11893 Z= 0.343 Chirality : 0.047 0.207 1360 Planarity : 0.004 0.035 1536 Dihedral : 4.069 19.925 1247 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.61 % Allowed : 30.15 % Favored : 66.24 % Cbeta Deviations : 0.09 % 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: -0.93 (0.25), residues: 1150 helix: 1.49 (0.36), residues: 220 sheet: -1.34 (0.28), residues: 318 loop : -0.95 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 402 HIS 0.014 0.001 HIS C 176 PHE 0.015 0.001 PHE E 100 TYR 0.010 0.001 TYR C 154 ARG 0.011 0.001 ARG E 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1982.43 seconds wall clock time: 37 minutes 20.65 seconds (2240.65 seconds total)