Starting phenix.real_space_refine on Sat Apr 6 08:43:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/04_2024/7sp6_25366.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/04_2024/7sp6_25366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/04_2024/7sp6_25366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/04_2024/7sp6_25366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/04_2024/7sp6_25366.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/04_2024/7sp6_25366.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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 1808 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 1 5.49 5 S 35 5.16 5 C 3858 2.51 5 N 977 2.21 5 O 1085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5957 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 4013 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 13, 'TRANS': 479} Chain breaks: 1 Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 916 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' MN': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.66 Number of scatterers: 5957 At special positions: 0 Unit cell: (72.36, 76.68, 155.52, 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) Mn 1 24.99 S 35 16.00 P 1 15.00 O 1085 8.00 N 977 7.00 C 3858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 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: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 46.8% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.646A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.946A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.539A pdb=" N ILE A 160 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.594A pdb=" N SER A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.683A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.938A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 5.236A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix removed outlier: 3.621A pdb=" N GLN A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.967A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 360 removed outlier: 4.485A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 392 removed outlier: 3.757A pdb=" N ILE A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.808A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.878A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 504 through 535 removed outlier: 3.590A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.566A pdb=" N LYS A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.704A pdb=" N TYR B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 removed outlier: 8.089A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 227 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.478A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.387A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.974A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR B 68 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 removed outlier: 7.457A pdb=" N THR B 121 " --> pdb=" O VAL B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.825A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.767A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 7 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 81 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 59 removed outlier: 4.336A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 33 " --> pdb=" O ARG C 98 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1024 1.33 - 1.45: 1741 1.45 - 1.57: 3268 1.57 - 1.69: 18 1.69 - 1.82: 53 Bond restraints: 6104 Sorted by residual: bond pdb=" CBD Y01 A 601 " pdb=" CBG Y01 A 601 " ideal model delta sigma weight residual 1.520 1.643 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" CAV Y01 A 601 " pdb=" CAZ Y01 A 601 " ideal model delta sigma weight residual 1.507 1.609 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 1.332 1.425 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" CAV Y01 A 601 " pdb=" CBC Y01 A 601 " ideal model delta sigma weight residual 1.523 1.613 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CBF Y01 A 601 " pdb=" CBH Y01 A 601 " ideal model delta sigma weight residual 1.550 1.639 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 6099 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.03: 98 106.03 - 113.03: 3208 113.03 - 120.03: 2101 120.03 - 127.03: 2796 127.03 - 134.03: 71 Bond angle restraints: 8274 Sorted by residual: angle pdb=" CAM Y01 A 601 " pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 111.19 124.33 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CAI Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CAV Y01 A 601 " ideal model delta sigma weight residual 120.03 131.73 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CAZ Y01 A 601 " pdb=" CAV Y01 A 601 " pdb=" CBC Y01 A 601 " ideal model delta sigma weight residual 111.19 122.29 -11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C ASN A 253 " pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 122.97 120.27 2.70 9.80e-01 1.04e+00 7.60e+00 angle pdb=" CAV Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CBH Y01 A 601 " ideal model delta sigma weight residual 116.96 108.83 8.13 3.00e+00 1.11e-01 7.34e+00 ... (remaining 8269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3265 17.95 - 35.89: 266 35.89 - 53.84: 63 53.84 - 71.78: 13 71.78 - 89.73: 7 Dihedral angle restraints: 3614 sinusoidal: 1479 harmonic: 2135 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 55.78 37.22 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -87.74 57.74 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP A 121 " pdb=" CB ASP A 121 " pdb=" CG ASP A 121 " pdb=" OD1 ASP A 121 " ideal model delta sinusoidal sigma weight residual -30.00 -83.41 53.41 1 2.00e+01 2.50e-03 9.69e+00 ... (remaining 3611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 837 0.080 - 0.159: 56 0.159 - 0.239: 1 0.239 - 0.318: 1 0.318 - 0.398: 3 Chirality restraints: 898 Sorted by residual: chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CBE Y01 A 601 " pdb=" CAP Y01 A 601 " pdb=" CBB Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.57 2.93 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CBI Y01 A 601 " pdb=" CAU Y01 A 601 " pdb=" CBE Y01 A 601 " pdb=" CBG Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 895 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 320 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 144 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.25e-01 pdb=" N PRO A 145 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 76 " 0.004 2.00e-02 2.50e+03 7.24e-03 5.24e-01 pdb=" C ASN C 76 " -0.013 2.00e-02 2.50e+03 pdb=" O ASN C 76 " 0.005 2.00e-02 2.50e+03 pdb=" N THR C 77 " 0.004 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1826 2.83 - 3.34: 5483 3.34 - 3.86: 9524 3.86 - 4.38: 10524 4.38 - 4.90: 18554 Nonbonded interactions: 45911 Sorted by model distance: nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.308 2.440 nonbonded pdb=" O TYR A 499 " pdb=" OH TYR A 507 " model vdw 2.355 2.440 nonbonded pdb=" OG SER C 51 " pdb=" O GLY C 56 " model vdw 2.358 2.440 nonbonded pdb=" ND2 ASN A 139 " pdb=" O LYS A 166 " model vdw 2.377 2.520 nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 183 " model vdw 2.379 2.440 ... (remaining 45906 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 individual isotropic 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 3.860 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.570 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.123 6104 Z= 0.294 Angle : 0.577 13.136 8274 Z= 0.253 Chirality : 0.045 0.398 898 Planarity : 0.002 0.031 1020 Dihedral : 14.433 89.727 2250 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.31), residues: 723 helix: 2.49 (0.30), residues: 302 sheet: 1.88 (0.45), residues: 135 loop : -0.78 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 53 HIS 0.000 0.000 HIS A 360 PHE 0.005 0.001 PHE C 37 TYR 0.011 0.001 TYR A 480 ARG 0.001 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.668 Fit side-chains REVERT: B 55 GLU cc_start: 0.8646 (mp0) cc_final: 0.8337 (mp0) REVERT: B 88 GLU cc_start: 0.7635 (pp20) cc_final: 0.7424 (mp0) REVERT: C 3 GLN cc_start: 0.8374 (mp-120) cc_final: 0.8172 (mm-40) REVERT: C 85 LEU cc_start: 0.8997 (mp) cc_final: 0.8758 (mp) REVERT: C 103 SER cc_start: 0.7719 (t) cc_final: 0.6861 (t) REVERT: C 118 GLN cc_start: 0.7834 (tp40) cc_final: 0.7564 (mm-40) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1603 time to fit residues: 25.6425 Evaluate side-chains 96 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6104 Z= 0.193 Angle : 0.490 5.195 8274 Z= 0.257 Chirality : 0.040 0.155 898 Planarity : 0.003 0.026 1020 Dihedral : 6.047 57.374 939 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.96 % Allowed : 8.65 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.31), residues: 723 helix: 2.50 (0.29), residues: 313 sheet: 1.48 (0.44), residues: 133 loop : -1.17 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 53 HIS 0.001 0.001 HIS A 552 PHE 0.022 0.001 PHE A 185 TYR 0.019 0.001 TYR A 46 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.720 Fit side-chains REVERT: B 3 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7387 (mm-40) REVERT: B 55 GLU cc_start: 0.8686 (mp0) cc_final: 0.8308 (mp0) REVERT: B 59 TYR cc_start: 0.8783 (m-80) cc_final: 0.8391 (m-10) REVERT: C 3 GLN cc_start: 0.8374 (mp-120) cc_final: 0.8153 (mm-40) REVERT: C 115 TYR cc_start: 0.8000 (m-10) cc_final: 0.7768 (m-10) REVERT: C 118 GLN cc_start: 0.7953 (tp40) cc_final: 0.7638 (mm-40) outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.1657 time to fit residues: 25.7120 Evaluate side-chains 93 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.0670 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6104 Z= 0.164 Angle : 0.455 5.556 8274 Z= 0.239 Chirality : 0.039 0.156 898 Planarity : 0.002 0.026 1020 Dihedral : 5.630 54.663 939 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.92 % Allowed : 15.54 % Favored : 82.53 % 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: 1.41 (0.31), residues: 723 helix: 2.52 (0.29), residues: 312 sheet: 1.38 (0.43), residues: 130 loop : -1.21 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.001 0.000 HIS A 360 PHE 0.015 0.001 PHE A 520 TYR 0.017 0.001 TYR A 550 ARG 0.001 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.725 Fit side-chains REVERT: A 242 MET cc_start: 0.7239 (ttt) cc_final: 0.6938 (ttt) REVERT: A 248 TYR cc_start: 0.6847 (m-10) cc_final: 0.6527 (m-80) REVERT: B 3 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7971 (mm110) REVERT: B 55 GLU cc_start: 0.8694 (mp0) cc_final: 0.8308 (mp0) REVERT: C 3 GLN cc_start: 0.8387 (mp-120) cc_final: 0.8134 (mm-40) REVERT: C 85 LEU cc_start: 0.8896 (mp) cc_final: 0.8576 (mp) REVERT: C 118 GLN cc_start: 0.7920 (tp40) cc_final: 0.7627 (mm-40) outliers start: 12 outliers final: 6 residues processed: 101 average time/residue: 0.1617 time to fit residues: 22.6299 Evaluate side-chains 94 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 0.0010 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6104 Z= 0.188 Angle : 0.482 5.720 8274 Z= 0.256 Chirality : 0.040 0.150 898 Planarity : 0.003 0.026 1020 Dihedral : 5.491 47.646 939 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.56 % Allowed : 16.03 % Favored : 81.41 % 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 (0.31), residues: 723 helix: 2.46 (0.29), residues: 312 sheet: 0.99 (0.41), residues: 140 loop : -1.22 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.001 HIS A 360 PHE 0.015 0.001 PHE A 427 TYR 0.014 0.001 TYR A 366 ARG 0.002 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.733 Fit side-chains REVERT: B 55 GLU cc_start: 0.8719 (mp0) cc_final: 0.8328 (mp0) REVERT: C 3 GLN cc_start: 0.8338 (mp-120) cc_final: 0.7982 (mm-40) outliers start: 16 outliers final: 9 residues processed: 108 average time/residue: 0.1780 time to fit residues: 25.5545 Evaluate side-chains 101 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6104 Z= 0.320 Angle : 0.593 7.022 8274 Z= 0.320 Chirality : 0.044 0.198 898 Planarity : 0.003 0.030 1020 Dihedral : 6.238 41.970 939 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.21 % Allowed : 16.83 % Favored : 79.97 % 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: 0.79 (0.30), residues: 723 helix: 2.12 (0.29), residues: 312 sheet: 0.58 (0.41), residues: 142 loop : -1.50 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 71 HIS 0.003 0.001 HIS A 174 PHE 0.015 0.002 PHE A 321 TYR 0.016 0.002 TYR C 93 ARG 0.006 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.678 Fit side-chains REVERT: A 266 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8038 (mm-40) REVERT: A 311 MET cc_start: 0.6366 (mmt) cc_final: 0.5917 (mtt) REVERT: B 55 GLU cc_start: 0.8734 (mp0) cc_final: 0.8342 (mp0) REVERT: C 3 GLN cc_start: 0.8293 (mp-120) cc_final: 0.7850 (mm-40) REVERT: C 71 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7550 (mtm110) outliers start: 20 outliers final: 15 residues processed: 110 average time/residue: 0.2002 time to fit residues: 28.6785 Evaluate side-chains 102 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6104 Z= 0.227 Angle : 0.529 7.483 8274 Z= 0.282 Chirality : 0.041 0.185 898 Planarity : 0.003 0.028 1020 Dihedral : 5.984 38.743 939 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.72 % Allowed : 18.27 % Favored : 79.01 % 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: 0.86 (0.30), residues: 723 helix: 2.22 (0.28), residues: 312 sheet: 0.55 (0.42), residues: 142 loop : -1.49 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.001 0.001 HIS A 174 PHE 0.012 0.001 PHE A 520 TYR 0.012 0.001 TYR A 414 ARG 0.007 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 266 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: A 311 MET cc_start: 0.6447 (mmt) cc_final: 0.6136 (mtt) REVERT: B 55 GLU cc_start: 0.8742 (mp0) cc_final: 0.8354 (mp0) REVERT: C 3 GLN cc_start: 0.8305 (mp-120) cc_final: 0.7834 (mm-40) outliers start: 17 outliers final: 12 residues processed: 102 average time/residue: 0.1732 time to fit residues: 23.5523 Evaluate side-chains 104 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.0170 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 0.0050 chunk 41 optimal weight: 0.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6104 Z= 0.152 Angle : 0.495 7.851 8274 Z= 0.259 Chirality : 0.040 0.181 898 Planarity : 0.003 0.028 1020 Dihedral : 5.660 37.184 939 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.40 % Allowed : 18.59 % Favored : 79.01 % 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 (0.31), residues: 723 helix: 2.37 (0.29), residues: 312 sheet: 0.56 (0.41), residues: 150 loop : -1.57 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 53 HIS 0.001 0.000 HIS A 174 PHE 0.012 0.001 PHE A 520 TYR 0.012 0.001 TYR A 414 ARG 0.005 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.678 Fit side-chains REVERT: A 266 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: A 311 MET cc_start: 0.6464 (mmt) cc_final: 0.6146 (mtt) REVERT: B 55 GLU cc_start: 0.8732 (mp0) cc_final: 0.8365 (mp0) REVERT: C 3 GLN cc_start: 0.8326 (mp-120) cc_final: 0.7795 (mm-40) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.1734 time to fit residues: 25.0522 Evaluate side-chains 105 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6104 Z= 0.185 Angle : 0.511 8.396 8274 Z= 0.271 Chirality : 0.041 0.233 898 Planarity : 0.003 0.031 1020 Dihedral : 5.626 36.976 939 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.88 % Allowed : 18.91 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.31), residues: 723 helix: 2.43 (0.28), residues: 312 sheet: 0.59 (0.40), residues: 150 loop : -1.54 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.011 0.001 PHE A 520 TYR 0.012 0.001 TYR A 414 ARG 0.007 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.712 Fit side-chains REVERT: A 311 MET cc_start: 0.6383 (mmt) cc_final: 0.6013 (mtt) REVERT: B 55 GLU cc_start: 0.8741 (mp0) cc_final: 0.8352 (mp0) REVERT: C 3 GLN cc_start: 0.8269 (mp-120) cc_final: 0.7768 (mm-40) outliers start: 18 outliers final: 15 residues processed: 109 average time/residue: 0.1964 time to fit residues: 28.5457 Evaluate side-chains 107 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6104 Z= 0.155 Angle : 0.511 8.555 8274 Z= 0.265 Chirality : 0.040 0.214 898 Planarity : 0.003 0.031 1020 Dihedral : 5.541 38.881 939 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.72 % Allowed : 19.23 % Favored : 78.04 % 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: 1.02 (0.31), residues: 723 helix: 2.51 (0.28), residues: 311 sheet: 0.49 (0.40), residues: 149 loop : -1.56 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.011 0.001 PHE A 520 TYR 0.013 0.001 TYR C 105 ARG 0.007 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.741 Fit side-chains REVERT: B 55 GLU cc_start: 0.8753 (mp0) cc_final: 0.8378 (mp0) REVERT: C 3 GLN cc_start: 0.8327 (mp-120) cc_final: 0.7759 (mm-40) outliers start: 17 outliers final: 16 residues processed: 110 average time/residue: 0.1866 time to fit residues: 27.1160 Evaluate side-chains 112 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6104 Z= 0.184 Angle : 0.512 8.799 8274 Z= 0.269 Chirality : 0.040 0.207 898 Planarity : 0.003 0.031 1020 Dihedral : 5.580 41.559 939 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.88 % Allowed : 19.23 % Favored : 77.88 % 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: 1.00 (0.31), residues: 723 helix: 2.50 (0.28), residues: 311 sheet: 0.47 (0.40), residues: 149 loop : -1.57 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.011 0.001 PHE A 520 TYR 0.018 0.001 TYR A 373 ARG 0.007 0.000 ARG B 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.789 Fit side-chains REVERT: B 55 GLU cc_start: 0.8757 (mp0) cc_final: 0.8384 (mp0) outliers start: 18 outliers final: 17 residues processed: 109 average time/residue: 0.1819 time to fit residues: 26.2389 Evaluate side-chains 109 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 0.0010 chunk 41 optimal weight: 6.9990 overall best weight: 0.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.098808 restraints weight = 9852.889| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.59 r_work: 0.3187 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6104 Z= 0.127 Angle : 0.485 8.639 8274 Z= 0.251 Chirality : 0.039 0.204 898 Planarity : 0.003 0.031 1020 Dihedral : 5.359 43.622 939 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.56 % Allowed : 19.07 % Favored : 78.37 % 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 (0.31), residues: 723 helix: 2.60 (0.28), residues: 311 sheet: 0.47 (0.40), residues: 149 loop : -1.55 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 53 HIS 0.001 0.000 HIS A 174 PHE 0.011 0.001 PHE A 520 TYR 0.017 0.001 TYR A 373 ARG 0.008 0.000 ARG B 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.04 seconds wall clock time: 31 minutes 28.71 seconds (1888.71 seconds total)