Starting phenix.real_space_refine on Thu Mar 14 23:31:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm9_13525/03_2024/7pm9_13525_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm9_13525/03_2024/7pm9_13525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm9_13525/03_2024/7pm9_13525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm9_13525/03_2024/7pm9_13525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm9_13525/03_2024/7pm9_13525_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm9_13525/03_2024/7pm9_13525_updated.pdb" } resolution = 3.7 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= 0.001 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 6422 2.51 5 N 1713 2.21 5 O 1883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10086 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6007 Classifications: {'peptide': 735} Link IDs: {'PTRANS': 27, 'TRANS': 707} Chain breaks: 6 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.87, per 1000 atoms: 0.58 Number of scatterers: 10086 At special positions: 0 Unit cell: (109.18, 137.8, 149.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 4 15.00 Mg 2 11.99 O 1883 8.00 N 1713 7.00 C 6422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2358 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 12 sheets defined 49.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.174A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.084A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.617A pdb=" N ALA A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 184 removed outlier: 3.621A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.571A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.886A pdb=" N GLY A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 removed outlier: 3.712A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.530A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.526A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 removed outlier: 3.769A pdb=" N ASP A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 479 removed outlier: 3.968A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.587A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.350A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 685 removed outlier: 3.743A pdb=" N VAL A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 704 through 710 Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 753 through 791 removed outlier: 4.802A pdb=" N ALA A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 784 " --> pdb=" O GLY A 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.610A pdb=" N LYS C 118 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 122 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU C 125 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.568A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.926A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.859A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.146A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.406A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.189A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.755A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.869A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 13 through 16 Processing sheet with id= C, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.580A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.571A pdb=" N ASN A 156 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS A 657 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= F, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= G, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.637A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= I, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= J, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 7.318A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 429 hydrogen bonds defined for protein. 1206 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: 3.07 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1676 1.32 - 1.44: 2735 1.44 - 1.56: 5784 1.56 - 1.69: 6 1.69 - 1.81: 100 Bond restraints: 10301 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.71e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.43e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 10296 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.70: 200 104.70 - 112.58: 5224 112.58 - 120.45: 4680 120.45 - 128.33: 3733 128.33 - 136.21: 80 Bond angle restraints: 13917 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.82 11.88 1.80e+00 3.09e-01 4.36e+01 angle pdb=" N LEU A 782 " pdb=" CA LEU A 782 " pdb=" C LEU A 782 " ideal model delta sigma weight residual 111.14 117.11 -5.97 1.08e+00 8.57e-01 3.05e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.77 -4.77 1.10e+00 8.26e-01 1.88e+01 angle pdb=" CA TYR A 787 " pdb=" CB TYR A 787 " pdb=" CG TYR A 787 " ideal model delta sigma weight residual 113.90 121.55 -7.65 1.80e+00 3.09e-01 1.81e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.08 8.02 1.90e+00 2.77e-01 1.78e+01 ... (remaining 13912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 6062 34.88 - 69.76: 108 69.76 - 104.64: 30 104.64 - 139.53: 4 139.53 - 174.41: 1 Dihedral angle restraints: 6205 sinusoidal: 2549 harmonic: 3656 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.40 -174.41 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 72.24 -132.24 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 172.66 127.34 1 2.00e+01 2.50e-03 3.86e+01 ... (remaining 6202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1102 0.050 - 0.101: 312 0.101 - 0.151: 92 0.151 - 0.202: 9 0.202 - 0.252: 5 Chirality restraints: 1520 Sorted by residual: chirality pdb=" CA MET A 648 " pdb=" N MET A 648 " pdb=" C MET A 648 " pdb=" CB MET A 648 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA TYR A 787 " pdb=" N TYR A 787 " pdb=" C TYR A 787 " pdb=" CB TYR A 787 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA HIS A 418 " pdb=" N HIS A 418 " pdb=" C HIS A 418 " pdb=" CB HIS A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1517 not shown) Planarity restraints: 1775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 116 " 0.138 9.50e-02 1.11e+02 7.90e-02 3.26e+01 pdb=" NE ARG C 116 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG C 116 " 0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG C 116 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG C 116 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.003 2.00e-02 2.50e+03 3.90e-02 3.04e+01 pdb=" CG TYR C 306 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.058 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 231 " 0.121 9.50e-02 1.11e+02 7.00e-02 2.64e+01 pdb=" NE ARG A 231 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 231 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG A 231 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 231 " -0.024 2.00e-02 2.50e+03 ... (remaining 1772 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 2 2.03 - 2.75: 1057 2.75 - 3.47: 14947 3.47 - 4.18: 23529 4.18 - 4.90: 41765 Nonbonded interactions: 81300 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.316 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.157 2.170 nonbonded pdb=" OH TYR A 100 " pdb=" OH TYR A 119 " model vdw 2.170 2.440 nonbonded pdb=" OG SER A 165 " pdb=" O ASN A 216 " model vdw 2.175 2.440 ... (remaining 81295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.020 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 30.570 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.005 0.122 10301 Z= 0.282 Angle : 0.928 11.883 13917 Z= 0.541 Chirality : 0.052 0.252 1520 Planarity : 0.008 0.085 1775 Dihedral : 16.173 174.408 3847 Min Nonbonded Distance : 1.316 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.81 % Cbeta Deviations : 0.08 % 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: -1.87 (0.20), residues: 1221 helix: -1.55 (0.16), residues: 614 sheet: 0.01 (0.41), residues: 141 loop : -0.92 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 356 HIS 0.007 0.001 HIS A 418 PHE 0.028 0.003 PHE C 266 TYR 0.059 0.007 TYR C 306 ARG 0.095 0.012 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8173 (p0) cc_final: 0.7937 (t70) REVERT: A 759 LEU cc_start: 0.9142 (mt) cc_final: 0.8774 (tt) REVERT: C 80 ASP cc_start: 0.7890 (p0) cc_final: 0.7686 (p0) outliers start: 1 outliers final: 1 residues processed: 178 average time/residue: 0.2516 time to fit residues: 60.9553 Evaluate side-chains 101 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 72 ASN A 156 ASN A 264 GLN A 395 HIS A 418 HIS A 525 GLN A 730 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 280 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10301 Z= 0.208 Angle : 0.658 10.788 13917 Z= 0.341 Chirality : 0.043 0.224 1520 Planarity : 0.004 0.051 1775 Dihedral : 10.459 165.222 1396 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.58 % Allowed : 5.77 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.27 (0.22), residues: 1221 helix: 0.41 (0.20), residues: 614 sheet: 0.62 (0.38), residues: 165 loop : -0.10 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 484 HIS 0.004 0.001 HIS A 354 PHE 0.021 0.002 PHE C 255 TYR 0.030 0.001 TYR A 787 ARG 0.007 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8114 (p0) cc_final: 0.7855 (t70) REVERT: A 305 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7842 (tmm) REVERT: A 633 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8733 (mmtt) REVERT: A 735 LEU cc_start: 0.8196 (mt) cc_final: 0.7811 (mt) REVERT: A 759 LEU cc_start: 0.9077 (mt) cc_final: 0.8764 (pp) outliers start: 17 outliers final: 9 residues processed: 126 average time/residue: 0.1986 time to fit residues: 37.2543 Evaluate side-chains 106 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS C 41 GLN C 78 ASN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10301 Z= 0.192 Angle : 0.594 13.135 13917 Z= 0.299 Chirality : 0.041 0.182 1520 Planarity : 0.004 0.042 1775 Dihedral : 9.014 126.821 1396 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.58 % Allowed : 7.91 % Favored : 90.50 % 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: 0.95 (0.23), residues: 1221 helix: 1.23 (0.21), residues: 600 sheet: 0.53 (0.38), residues: 165 loop : 0.01 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.017 0.001 PHE C 255 TYR 0.026 0.001 TYR A 787 ARG 0.004 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8091 (p0) cc_final: 0.7856 (t70) REVERT: B 120 MET cc_start: 0.7929 (ttt) cc_final: 0.7192 (tpt) REVERT: A 305 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7789 (tmm) REVERT: A 633 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8735 (mmtt) REVERT: A 759 LEU cc_start: 0.9052 (mt) cc_final: 0.8768 (pp) REVERT: A 767 LEU cc_start: 0.8838 (pp) cc_final: 0.8383 (tt) outliers start: 17 outliers final: 9 residues processed: 111 average time/residue: 0.2054 time to fit residues: 34.4324 Evaluate side-chains 95 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.0670 chunk 119 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10301 Z= 0.164 Angle : 0.574 11.625 13917 Z= 0.282 Chirality : 0.041 0.190 1520 Planarity : 0.003 0.036 1775 Dihedral : 7.562 94.009 1396 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.21 % Allowed : 8.85 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1221 helix: 1.42 (0.21), residues: 601 sheet: 0.55 (0.37), residues: 159 loop : 0.04 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.004 0.001 HIS C 161 PHE 0.016 0.001 PHE C 255 TYR 0.022 0.001 TYR A 787 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7946 (ttt) cc_final: 0.6975 (tpt) REVERT: A 364 MET cc_start: 0.8734 (mmm) cc_final: 0.8524 (mmp) REVERT: A 759 LEU cc_start: 0.9047 (mt) cc_final: 0.8784 (pp) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.2237 time to fit residues: 35.7805 Evaluate side-chains 92 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 80 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 0.0070 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 88 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10301 Z= 0.162 Angle : 0.566 8.749 13917 Z= 0.275 Chirality : 0.040 0.184 1520 Planarity : 0.003 0.037 1775 Dihedral : 6.887 77.395 1396 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.49 % Allowed : 10.24 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1221 helix: 1.55 (0.22), residues: 600 sheet: 0.36 (0.37), residues: 162 loop : 0.09 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 484 HIS 0.004 0.001 HIS A 354 PHE 0.015 0.001 PHE C 255 TYR 0.020 0.001 TYR A 787 ARG 0.005 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7817 (ttt) cc_final: 0.6823 (tpt) REVERT: A 759 LEU cc_start: 0.9076 (mt) cc_final: 0.8827 (pp) outliers start: 16 outliers final: 8 residues processed: 104 average time/residue: 0.1991 time to fit residues: 31.1580 Evaluate side-chains 90 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 0.2980 chunk 99 optimal weight: 0.0870 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10301 Z= 0.150 Angle : 0.569 11.036 13917 Z= 0.272 Chirality : 0.039 0.170 1520 Planarity : 0.003 0.038 1775 Dihedral : 6.387 74.924 1395 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.49 % Allowed : 10.52 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1221 helix: 1.63 (0.22), residues: 600 sheet: 0.38 (0.37), residues: 161 loop : 0.12 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.004 0.001 HIS C 161 PHE 0.015 0.001 PHE C 255 TYR 0.019 0.001 TYR A 787 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 CYS cc_start: 0.3644 (OUTLIER) cc_final: 0.3126 (p) REVERT: B 120 MET cc_start: 0.7579 (ttt) cc_final: 0.6585 (tpp) REVERT: A 759 LEU cc_start: 0.9082 (mt) cc_final: 0.8836 (pp) REVERT: A 783 MET cc_start: 0.4816 (mpp) cc_final: 0.4584 (mmp) outliers start: 16 outliers final: 9 residues processed: 104 average time/residue: 0.1721 time to fit residues: 27.0899 Evaluate side-chains 94 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 0.0000 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10301 Z= 0.145 Angle : 0.562 12.610 13917 Z= 0.269 Chirality : 0.040 0.167 1520 Planarity : 0.003 0.039 1775 Dihedral : 6.255 77.125 1395 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.58 % Allowed : 11.08 % Favored : 87.34 % 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: 1.33 (0.24), residues: 1221 helix: 1.67 (0.22), residues: 593 sheet: 0.44 (0.38), residues: 161 loop : 0.15 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.004 0.001 HIS C 161 PHE 0.014 0.001 PHE C 255 TYR 0.018 0.001 TYR A 787 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 CYS cc_start: 0.3495 (OUTLIER) cc_final: 0.2947 (p) REVERT: B 120 MET cc_start: 0.7634 (ttt) cc_final: 0.6656 (tpp) REVERT: A 671 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7376 (t80) REVERT: A 759 LEU cc_start: 0.9072 (mt) cc_final: 0.8832 (pp) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.2018 time to fit residues: 29.8952 Evaluate side-chains 89 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 88 ASN A 418 HIS ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10301 Z= 0.184 Angle : 0.591 11.117 13917 Z= 0.281 Chirality : 0.040 0.167 1520 Planarity : 0.003 0.041 1775 Dihedral : 6.277 77.253 1395 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.40 % Allowed : 11.82 % Favored : 86.78 % 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: 1.37 (0.24), residues: 1221 helix: 1.70 (0.22), residues: 599 sheet: 0.38 (0.39), residues: 161 loop : 0.17 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 484 HIS 0.009 0.001 HIS A 418 PHE 0.014 0.001 PHE C 255 TYR 0.020 0.001 TYR A 787 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 CYS cc_start: 0.3935 (OUTLIER) cc_final: 0.3508 (p) REVERT: B 120 MET cc_start: 0.7470 (ttt) cc_final: 0.6921 (tpp) REVERT: A 239 MET cc_start: 0.7815 (mmm) cc_final: 0.7598 (tmm) REVERT: A 305 MET cc_start: 0.8082 (tmm) cc_final: 0.7812 (tmm) REVERT: A 671 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7342 (t80) REVERT: A 759 LEU cc_start: 0.9046 (mt) cc_final: 0.8778 (pp) REVERT: C 202 THR cc_start: 0.7688 (t) cc_final: 0.7453 (p) outliers start: 15 outliers final: 10 residues processed: 94 average time/residue: 0.1956 time to fit residues: 28.1419 Evaluate side-chains 91 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.0040 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10301 Z= 0.157 Angle : 0.602 11.097 13917 Z= 0.285 Chirality : 0.040 0.171 1520 Planarity : 0.003 0.040 1775 Dihedral : 6.190 77.531 1395 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.12 % Allowed : 12.38 % Favored : 86.50 % 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: 1.43 (0.25), residues: 1221 helix: 1.71 (0.22), residues: 603 sheet: 0.42 (0.39), residues: 161 loop : 0.25 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 PHE 0.020 0.001 PHE B 12 TYR 0.016 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7417 (ttt) cc_final: 0.6785 (tpp) REVERT: A 305 MET cc_start: 0.8078 (tmm) cc_final: 0.7783 (tmm) REVERT: A 671 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7408 (t80) REVERT: A 759 LEU cc_start: 0.9031 (mt) cc_final: 0.8767 (pp) REVERT: A 783 MET cc_start: 0.3842 (mmt) cc_final: 0.3571 (mmp) outliers start: 12 outliers final: 9 residues processed: 93 average time/residue: 0.1875 time to fit residues: 27.1715 Evaluate side-chains 88 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.4980 chunk 71 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 113 optimal weight: 0.0170 chunk 98 optimal weight: 0.4980 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10301 Z= 0.157 Angle : 0.604 10.887 13917 Z= 0.287 Chirality : 0.040 0.207 1520 Planarity : 0.004 0.042 1775 Dihedral : 6.141 77.601 1395 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.12 % Allowed : 12.85 % Favored : 86.03 % 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: 1.52 (0.25), residues: 1221 helix: 1.82 (0.23), residues: 596 sheet: 0.32 (0.39), residues: 161 loop : 0.31 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 484 HIS 0.004 0.001 HIS A 354 PHE 0.021 0.001 PHE B 12 TYR 0.016 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7157 (ttt) cc_final: 0.6576 (tpp) REVERT: A 305 MET cc_start: 0.8073 (tmm) cc_final: 0.7780 (tmm) REVERT: A 759 LEU cc_start: 0.9026 (mt) cc_final: 0.8775 (pp) REVERT: A 783 MET cc_start: 0.3960 (mmt) cc_final: 0.3721 (mmp) outliers start: 12 outliers final: 11 residues processed: 90 average time/residue: 0.1867 time to fit residues: 25.9119 Evaluate side-chains 87 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0040 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.065904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048514 restraints weight = 47755.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.050151 restraints weight = 24598.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051233 restraints weight = 15626.835| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10301 Z= 0.157 Angle : 0.589 10.097 13917 Z= 0.280 Chirality : 0.040 0.203 1520 Planarity : 0.003 0.042 1775 Dihedral : 6.116 77.756 1395 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.02 % Allowed : 13.04 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1221 helix: 1.82 (0.23), residues: 596 sheet: 0.30 (0.40), residues: 161 loop : 0.31 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.004 0.001 HIS C 161 PHE 0.018 0.001 PHE B 12 TYR 0.015 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2104.88 seconds wall clock time: 39 minutes 1.14 seconds (2341.14 seconds total)