Starting phenix.real_space_refine on Tue Feb 13 17:56:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/02_2024/6vz1_21481_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/02_2024/6vz1_21481.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/02_2024/6vz1_21481_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/02_2024/6vz1_21481_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/02_2024/6vz1_21481_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/02_2024/6vz1_21481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/02_2024/6vz1_21481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/02_2024/6vz1_21481_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/02_2024/6vz1_21481_updated.pdb" } resolution = 3.2 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 44 5.16 5 C 4736 2.51 5 N 1160 2.21 5 O 1162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7112 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3391 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3391 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 165 Unusual residues: {'3VV': 1, '6OU': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 165 Unusual residues: {'3VV': 1, '6OU': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.27, per 1000 atoms: 0.60 Number of scatterers: 7112 At special positions: 0 Unit cell: (107.07, 94.62, 82.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 10 15.00 O 1162 8.00 N 1160 7.00 C 4736 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 103 through 110 removed outlier: 3.833A pdb=" N ILE A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 132 through 156 removed outlier: 4.412A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 185 removed outlier: 3.606A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix removed outlier: 4.286A pdb=" N LEU A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.963A pdb=" N LEU A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 227 removed outlier: 3.592A pdb=" N SER A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 249 through 257 Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.750A pdb=" N GLN A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.026A pdb=" N GLN A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.665A pdb=" N ARG A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 400 through 418 Processing helix chain 'A' and resid 430 through 447 removed outlier: 3.687A pdb=" N GLN A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix removed outlier: 3.806A pdb=" N PHE A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.530A pdb=" N ASN A 454 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 461 " --> pdb=" O TRP A 458 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 463 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.638A pdb=" N VAL A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 88 through 100 Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.833A pdb=" N ILE B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 132 through 156 removed outlier: 4.412A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 185 removed outlier: 3.606A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Proline residue: B 179 - end of helix removed outlier: 4.287A pdb=" N LEU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.964A pdb=" N LEU B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 227 removed outlier: 3.592A pdb=" N SER B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 249 through 257 Processing helix chain 'B' and resid 275 through 298 removed outlier: 3.750A pdb=" N GLN B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 327 through 341 Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.026A pdb=" N GLN B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 3.665A pdb=" N ARG B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 400 through 418 Processing helix chain 'B' and resid 430 through 447 removed outlier: 3.687A pdb=" N GLN B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Proline residue: B 439 - end of helix removed outlier: 3.805A pdb=" N PHE B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 4.530A pdb=" N ASN B 454 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 461 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 463 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 480 removed outlier: 3.638A pdb=" N VAL B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 480 " --> pdb=" O TYR B 476 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1000 1.31 - 1.43: 2216 1.43 - 1.56: 4022 1.56 - 1.69: 18 1.69 - 1.81: 72 Bond restraints: 7328 Sorted by residual: bond pdb=" C49 3VV B 503 " pdb=" C50 3VV B 503 " ideal model delta sigma weight residual 1.291 1.561 -0.270 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C49 3VV A 503 " pdb=" C50 3VV A 503 " ideal model delta sigma weight residual 1.291 1.541 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C49 3VV B 503 " pdb=" O48 3VV B 503 " ideal model delta sigma weight residual 1.621 1.414 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C49 3VV A 503 " pdb=" O48 3VV A 503 " ideal model delta sigma weight residual 1.621 1.416 0.205 2.00e-02 2.50e+03 1.06e+02 bond pdb=" O37 3VV B 503 " pdb=" P38 3VV B 503 " ideal model delta sigma weight residual 1.662 1.504 0.158 2.00e-02 2.50e+03 6.23e+01 ... (remaining 7323 not shown) Histogram of bond angle deviations from ideal: 84.85 - 94.71: 1 94.71 - 104.56: 135 104.56 - 114.42: 4365 114.42 - 124.28: 5191 124.28 - 134.13: 236 Bond angle restraints: 9928 Sorted by residual: angle pdb=" C09 3VV A 503 " pdb=" C10 3VV A 503 " pdb=" C11 3VV A 503 " ideal model delta sigma weight residual 152.65 125.61 27.04 3.00e+00 1.11e-01 8.12e+01 angle pdb=" C09 3VV B 503 " pdb=" C10 3VV B 503 " pdb=" C11 3VV B 503 " ideal model delta sigma weight residual 152.65 127.97 24.68 3.00e+00 1.11e-01 6.77e+01 angle pdb=" O37 3VV B 503 " pdb=" P38 3VV B 503 " pdb=" O41 3VV B 503 " ideal model delta sigma weight residual 109.45 84.85 24.60 3.00e+00 1.11e-01 6.72e+01 angle pdb=" C21 6OU A 501 " pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " ideal model delta sigma weight residual 117.17 133.97 -16.80 3.00e+00 1.11e-01 3.14e+01 angle pdb=" C21 6OU B 501 " pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " ideal model delta sigma weight residual 117.17 133.71 -16.54 3.00e+00 1.11e-01 3.04e+01 ... (remaining 9923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 4154 35.31 - 70.61: 113 70.61 - 105.92: 20 105.92 - 141.22: 15 141.22 - 176.53: 4 Dihedral angle restraints: 4306 sinusoidal: 1864 harmonic: 2442 Sorted by residual: dihedral pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLY B 87 " pdb=" C GLY B 87 " pdb=" N ILE B 88 " pdb=" CA ILE B 88 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" C34 6OU A 502 " pdb=" C31 6OU A 502 " pdb=" C33 6OU A 502 " pdb=" O30 6OU A 502 " ideal model delta sinusoidal sigma weight residual 180.29 3.76 176.53 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1029 0.123 - 0.247: 17 0.247 - 0.370: 4 0.370 - 0.494: 1 0.494 - 0.617: 1 Chirality restraints: 1052 Sorted by residual: chirality pdb=" C31 3VV B 503 " pdb=" C29 3VV B 503 " pdb=" C33 3VV B 503 " pdb=" O32 3VV B 503 " both_signs ideal model delta sigma weight residual False -2.53 -1.92 -0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" C31 3VV A 503 " pdb=" C29 3VV A 503 " pdb=" C33 3VV A 503 " pdb=" O32 3VV A 503 " both_signs ideal model delta sigma weight residual False -2.53 -2.14 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C50 3VV A 503 " pdb=" C49 3VV A 503 " pdb=" C52 3VV A 503 " pdb=" O51 3VV A 503 " both_signs ideal model delta sigma weight residual False -2.38 -2.69 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 1049 not shown) Planarity restraints: 1196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C49 3VV B 503 " -0.227 2.00e-02 2.50e+03 9.67e-02 2.57e+02 pdb=" C59 3VV B 503 " 0.076 2.00e-02 2.50e+03 pdb=" C61 3VV B 503 " 0.046 2.00e-02 2.50e+03 pdb=" C62 3VV B 503 " -0.039 2.00e-02 2.50e+03 pdb=" C65 3VV B 503 " 0.045 2.00e-02 2.50e+03 pdb=" C67 3VV B 503 " 0.067 2.00e-02 2.50e+03 pdb=" N58 3VV B 503 " 0.029 2.00e-02 2.50e+03 pdb=" N60 3VV B 503 " 0.080 2.00e-02 2.50e+03 pdb=" N63 3VV B 503 " -0.131 2.00e-02 2.50e+03 pdb=" N64 3VV B 503 " -0.043 2.00e-02 2.50e+03 pdb=" N66 3VV B 503 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 3VV B 503 " 0.061 2.00e-02 2.50e+03 4.98e-02 3.10e+01 pdb=" C24 3VV B 503 " -0.034 2.00e-02 2.50e+03 pdb=" C26 3VV B 503 " 0.052 2.00e-02 2.50e+03 pdb=" N23 3VV B 503 " -0.069 2.00e-02 2.50e+03 pdb=" O25 3VV B 503 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 3VV A 503 " -0.048 2.00e-02 2.50e+03 3.93e-02 1.93e+01 pdb=" C29 3VV A 503 " 0.016 2.00e-02 2.50e+03 pdb=" C31 3VV A 503 " -0.037 2.00e-02 2.50e+03 pdb=" N28 3VV A 503 " 0.061 2.00e-02 2.50e+03 pdb=" O30 3VV A 503 " 0.008 2.00e-02 2.50e+03 ... (remaining 1193 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 37 2.47 - 3.08: 5094 3.08 - 3.69: 10536 3.69 - 4.29: 15820 4.29 - 4.90: 26139 Nonbonded interactions: 57626 Sorted by model distance: nonbonded pdb=" OH TYR B 390 " pdb=" O43 3VV B 503 " model vdw 1.864 2.440 nonbonded pdb=" O GLU B 416 " pdb=" OG SER B 420 " model vdw 2.065 2.440 nonbonded pdb=" O GLU A 416 " pdb=" OG SER A 420 " model vdw 2.065 2.440 nonbonded pdb=" O39 3VV B 503 " pdb=" O45 3VV B 503 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 390 " pdb=" O43 3VV A 503 " model vdw 2.216 2.440 ... (remaining 57621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.000 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: 3.940 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.900 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.014 0.270 7328 Z= 0.886 Angle : 1.252 27.037 9928 Z= 0.532 Chirality : 0.059 0.617 1052 Planarity : 0.006 0.097 1196 Dihedral : 20.456 176.527 2722 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % 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: -4.38 (0.25), residues: 814 helix: -2.37 (0.18), residues: 590 sheet: None (None), residues: 0 loop : -3.92 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 377 HIS 0.012 0.002 HIS B 168 PHE 0.021 0.002 PHE A 277 TYR 0.019 0.002 TYR B 417 ARG 0.003 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.779 Fit side-chains REVERT: A 79 ASP cc_start: 0.8120 (p0) cc_final: 0.7901 (p0) REVERT: A 387 ARG cc_start: 0.7783 (mmm160) cc_final: 0.7532 (ttt180) REVERT: A 395 ARG cc_start: 0.8313 (ttm110) cc_final: 0.8026 (ttm-80) REVERT: A 427 ARG cc_start: 0.7799 (mpt90) cc_final: 0.7496 (mmm160) REVERT: A 434 MET cc_start: 0.7667 (mmm) cc_final: 0.7375 (mmt) REVERT: B 340 TRP cc_start: 0.8428 (t60) cc_final: 0.8205 (t60) REVERT: B 387 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7570 (ttt180) REVERT: B 434 MET cc_start: 0.7660 (mmm) cc_final: 0.7277 (mmt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2176 time to fit residues: 37.8336 Evaluate side-chains 99 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 246 ASN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 246 ASN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7328 Z= 0.166 Angle : 0.588 8.580 9928 Z= 0.283 Chirality : 0.041 0.303 1052 Planarity : 0.004 0.034 1196 Dihedral : 20.712 178.390 1166 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.95 % Allowed : 11.28 % Favored : 86.77 % 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: -2.45 (0.28), residues: 814 helix: -0.92 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.35 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 131 HIS 0.002 0.001 HIS A 168 PHE 0.013 0.001 PHE B 443 TYR 0.009 0.001 TYR A 339 ARG 0.004 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.791 Fit side-chains REVERT: A 246 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8535 (p0) REVERT: A 285 MET cc_start: 0.8364 (mtp) cc_final: 0.8095 (mtp) REVERT: A 387 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7485 (ttt180) REVERT: A 425 MET cc_start: 0.8296 (mtp) cc_final: 0.8072 (mtp) REVERT: A 427 ARG cc_start: 0.7646 (mpt90) cc_final: 0.7390 (mmm160) REVERT: A 447 PHE cc_start: 0.7561 (m-10) cc_final: 0.7344 (m-10) REVERT: B 151 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8431 (tp30) REVERT: B 285 MET cc_start: 0.8423 (mtp) cc_final: 0.8215 (mtp) REVERT: B 290 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8417 (tm-30) REVERT: B 363 ASP cc_start: 0.8941 (p0) cc_final: 0.8559 (p0) REVERT: B 387 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7400 (ttt180) REVERT: B 427 ARG cc_start: 0.7848 (mmt-90) cc_final: 0.7243 (mmm160) outliers start: 14 outliers final: 9 residues processed: 140 average time/residue: 0.1799 time to fit residues: 34.1794 Evaluate side-chains 123 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 50 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7328 Z= 0.154 Angle : 0.563 9.459 9928 Z= 0.269 Chirality : 0.039 0.168 1052 Planarity : 0.004 0.030 1196 Dihedral : 19.729 178.915 1166 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.53 % Allowed : 14.90 % Favored : 83.57 % 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: -1.67 (0.30), residues: 814 helix: -0.26 (0.22), residues: 586 sheet: None (None), residues: 0 loop : -3.25 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.004 0.000 HIS B 415 PHE 0.015 0.001 PHE B 443 TYR 0.011 0.001 TYR A 339 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.698 Fit side-chains REVERT: A 102 ARG cc_start: 0.7748 (ptm-80) cc_final: 0.7095 (ttp-170) REVERT: A 341 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8343 (tt) REVERT: A 387 ARG cc_start: 0.7694 (mmm160) cc_final: 0.7439 (ttt180) REVERT: A 427 ARG cc_start: 0.7609 (mpt90) cc_final: 0.7340 (mmm160) REVERT: B 102 ARG cc_start: 0.7748 (ptm-80) cc_final: 0.7055 (ttp-170) REVERT: B 162 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7608 (mm-40) REVERT: B 290 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8498 (tm-30) REVERT: B 341 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8321 (tt) REVERT: B 387 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7463 (ttt180) REVERT: B 427 ARG cc_start: 0.7756 (mmt-90) cc_final: 0.7180 (mmm160) outliers start: 11 outliers final: 9 residues processed: 128 average time/residue: 0.1991 time to fit residues: 34.0193 Evaluate side-chains 123 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 341 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 246 ASN A 366 ASN B 168 HIS B 366 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 7328 Z= 0.484 Angle : 0.704 9.458 9928 Z= 0.341 Chirality : 0.046 0.161 1052 Planarity : 0.005 0.033 1196 Dihedral : 20.464 179.278 1166 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.48 % Allowed : 15.60 % Favored : 80.92 % 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: -2.03 (0.29), residues: 814 helix: -0.60 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.21 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.016 0.002 HIS A 168 PHE 0.018 0.002 PHE B 443 TYR 0.017 0.002 TYR B 417 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.715 Fit side-chains REVERT: A 151 GLU cc_start: 0.8797 (tp30) cc_final: 0.8568 (tp30) REVERT: A 162 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7655 (mm-40) REVERT: A 246 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8458 (p0) REVERT: A 298 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.6972 (mp10) REVERT: A 341 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8471 (tt) REVERT: A 387 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7477 (ttt180) REVERT: A 427 ARG cc_start: 0.7808 (mpt90) cc_final: 0.7337 (mmm160) REVERT: A 435 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7486 (mtm) REVERT: B 298 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7130 (mp-120) REVERT: B 341 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8416 (tt) REVERT: B 387 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7480 (ttt180) outliers start: 25 outliers final: 15 residues processed: 131 average time/residue: 0.1631 time to fit residues: 29.5451 Evaluate side-chains 129 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 341 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7328 Z= 0.153 Angle : 0.555 9.882 9928 Z= 0.266 Chirality : 0.038 0.121 1052 Planarity : 0.004 0.031 1196 Dihedral : 19.352 179.583 1166 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.53 % Allowed : 18.25 % Favored : 80.22 % 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: -1.34 (0.30), residues: 814 helix: 0.04 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -3.23 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.002 0.000 HIS B 415 PHE 0.015 0.001 PHE A 443 TYR 0.010 0.001 TYR A 339 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.693 Fit side-chains REVERT: A 102 ARG cc_start: 0.7685 (ptm-80) cc_final: 0.6569 (ptt180) REVERT: A 162 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7564 (mm-40) REVERT: A 341 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 387 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7443 (ttt180) REVERT: A 427 ARG cc_start: 0.7567 (mpt90) cc_final: 0.7339 (mmm160) REVERT: A 435 MET cc_start: 0.7706 (mtp) cc_final: 0.7470 (mtm) REVERT: B 102 ARG cc_start: 0.7674 (ptm-80) cc_final: 0.7032 (ttp-170) REVERT: B 162 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7582 (mm-40) REVERT: B 387 ARG cc_start: 0.7738 (mmm160) cc_final: 0.7457 (ttt180) REVERT: B 427 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7277 (mmm160) outliers start: 11 outliers final: 6 residues processed: 123 average time/residue: 0.2177 time to fit residues: 35.0082 Evaluate side-chains 119 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7328 Z= 0.264 Angle : 0.588 8.910 9928 Z= 0.283 Chirality : 0.040 0.118 1052 Planarity : 0.004 0.030 1196 Dihedral : 19.205 177.726 1166 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.23 % Allowed : 18.38 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.29), residues: 814 helix: -0.04 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.41 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 340 HIS 0.003 0.001 HIS B 415 PHE 0.017 0.001 PHE A 443 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.818 Fit side-chains REVERT: A 162 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7656 (mm-40) REVERT: A 341 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8353 (tt) REVERT: A 387 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7449 (ttt180) REVERT: A 427 ARG cc_start: 0.7563 (mpt90) cc_final: 0.7116 (mmm160) REVERT: A 435 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7450 (mtm) REVERT: B 102 ARG cc_start: 0.7669 (ptm-80) cc_final: 0.7033 (ttp-170) REVERT: B 298 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.6849 (mp10) REVERT: B 341 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8353 (tt) REVERT: B 387 ARG cc_start: 0.7743 (mmm160) cc_final: 0.7467 (ttt180) REVERT: B 427 ARG cc_start: 0.7897 (mmt-90) cc_final: 0.7277 (mmm160) outliers start: 16 outliers final: 11 residues processed: 120 average time/residue: 0.1918 time to fit residues: 31.1269 Evaluate side-chains 123 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7328 Z= 0.169 Angle : 0.553 10.496 9928 Z= 0.263 Chirality : 0.038 0.113 1052 Planarity : 0.004 0.029 1196 Dihedral : 18.275 173.359 1166 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.37 % Allowed : 19.08 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.30), residues: 814 helix: 0.20 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.37 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 340 HIS 0.002 0.000 HIS B 415 PHE 0.016 0.001 PHE A 443 TYR 0.010 0.001 TYR A 339 ARG 0.001 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.705 Fit side-chains REVERT: A 102 ARG cc_start: 0.7648 (ptm-80) cc_final: 0.6559 (ptt180) REVERT: A 162 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7653 (mm-40) REVERT: A 298 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: A 341 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8323 (tt) REVERT: A 387 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7448 (ttt180) REVERT: A 427 ARG cc_start: 0.7470 (mpt90) cc_final: 0.7033 (mmm160) REVERT: A 435 MET cc_start: 0.7701 (mtp) cc_final: 0.7434 (mtm) REVERT: B 102 ARG cc_start: 0.7579 (ptm-80) cc_final: 0.6931 (ttp-170) REVERT: B 298 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.6837 (mp10) REVERT: B 341 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 387 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7435 (ttt180) REVERT: B 427 ARG cc_start: 0.7791 (mmt-90) cc_final: 0.7246 (mmm160) outliers start: 17 outliers final: 12 residues processed: 130 average time/residue: 0.1953 time to fit residues: 34.0663 Evaluate side-chains 131 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7328 Z= 0.348 Angle : 0.635 9.828 9928 Z= 0.304 Chirality : 0.042 0.127 1052 Planarity : 0.004 0.029 1196 Dihedral : 18.838 179.402 1166 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.79 % Allowed : 19.50 % Favored : 77.72 % 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: -1.31 (0.29), residues: 814 helix: 0.04 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.33 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 340 HIS 0.004 0.001 HIS B 415 PHE 0.017 0.002 PHE A 443 TYR 0.013 0.001 TYR B 417 ARG 0.002 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.788 Fit side-chains REVERT: A 298 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.6962 (mp10) REVERT: A 341 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 387 ARG cc_start: 0.7776 (mmm160) cc_final: 0.7465 (ttt180) REVERT: A 427 ARG cc_start: 0.7566 (mpt90) cc_final: 0.7090 (mmm160) REVERT: A 435 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7434 (mtm) REVERT: B 102 ARG cc_start: 0.7640 (ptm-80) cc_final: 0.6567 (ptt180) REVERT: B 298 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.6842 (mp10) REVERT: B 341 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8322 (tt) REVERT: B 387 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7476 (ttt180) outliers start: 20 outliers final: 12 residues processed: 121 average time/residue: 0.1865 time to fit residues: 30.9800 Evaluate side-chains 123 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7328 Z= 0.225 Angle : 0.588 10.411 9928 Z= 0.280 Chirality : 0.040 0.116 1052 Planarity : 0.004 0.029 1196 Dihedral : 18.338 177.816 1166 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.79 % Allowed : 19.64 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.30), residues: 814 helix: 0.18 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.29 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 340 HIS 0.002 0.001 HIS B 415 PHE 0.017 0.001 PHE A 443 TYR 0.012 0.001 TYR B 339 ARG 0.001 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.764 Fit side-chains REVERT: A 298 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: A 341 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8404 (tt) REVERT: A 387 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7457 (ttt180) REVERT: A 427 ARG cc_start: 0.7430 (mpt90) cc_final: 0.6932 (mmm160) REVERT: A 435 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7443 (mtm) REVERT: B 102 ARG cc_start: 0.7519 (ptm-80) cc_final: 0.6463 (ptt180) REVERT: B 298 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.6833 (mp10) REVERT: B 341 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8306 (tt) REVERT: B 387 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7456 (ttt180) outliers start: 20 outliers final: 12 residues processed: 123 average time/residue: 0.1838 time to fit residues: 30.9287 Evaluate side-chains 125 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7328 Z= 0.151 Angle : 0.554 10.238 9928 Z= 0.262 Chirality : 0.037 0.112 1052 Planarity : 0.004 0.030 1196 Dihedral : 17.232 170.207 1166 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.09 % Allowed : 20.61 % Favored : 77.30 % 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: -0.85 (0.30), residues: 814 helix: 0.47 (0.23), residues: 590 sheet: None (None), residues: 0 loop : -3.39 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 340 HIS 0.001 0.000 HIS B 168 PHE 0.016 0.001 PHE A 443 TYR 0.011 0.001 TYR B 339 ARG 0.002 0.000 ARG B 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.862 Fit side-chains REVERT: A 102 ARG cc_start: 0.7581 (ptm-80) cc_final: 0.6521 (ptt180) REVERT: A 298 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.6915 (mp10) REVERT: A 341 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8310 (tt) REVERT: A 387 ARG cc_start: 0.7734 (mmm160) cc_final: 0.7434 (ttt180) REVERT: A 402 MET cc_start: 0.8265 (ttm) cc_final: 0.8038 (ttm) REVERT: A 427 ARG cc_start: 0.7306 (mpt90) cc_final: 0.6826 (mmm160) REVERT: B 298 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.6808 (mp10) REVERT: B 316 TYR cc_start: 0.5886 (m-10) cc_final: 0.5311 (p90) REVERT: B 341 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8326 (tt) REVERT: B 387 ARG cc_start: 0.7721 (mmm160) cc_final: 0.7485 (ttt180) REVERT: B 402 MET cc_start: 0.8253 (ttm) cc_final: 0.7985 (ttm) REVERT: B 427 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.6998 (mmm160) outliers start: 15 outliers final: 8 residues processed: 126 average time/residue: 0.2308 time to fit residues: 39.6056 Evaluate side-chains 115 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 47 optimal weight: 0.2980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116264 restraints weight = 9005.165| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.11 r_work: 0.3261 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7328 Z= 0.136 Angle : 0.542 10.028 9928 Z= 0.254 Chirality : 0.037 0.110 1052 Planarity : 0.004 0.031 1196 Dihedral : 16.289 167.783 1166 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.95 % Allowed : 21.17 % Favored : 76.88 % 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: -0.68 (0.30), residues: 814 helix: 0.62 (0.23), residues: 586 sheet: None (None), residues: 0 loop : -3.37 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 340 HIS 0.001 0.000 HIS B 168 PHE 0.016 0.001 PHE A 443 TYR 0.011 0.001 TYR B 339 ARG 0.003 0.000 ARG A 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1718.33 seconds wall clock time: 32 minutes 3.66 seconds (1923.66 seconds total)