Starting phenix.real_space_refine on Wed Feb 14 16:01:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/02_2024/8a8c_15229_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/02_2024/8a8c_15229.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/02_2024/8a8c_15229_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/02_2024/8a8c_15229_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/02_2024/8a8c_15229_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/02_2024/8a8c_15229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/02_2024/8a8c_15229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/02_2024/8a8c_15229_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/02_2024/8a8c_15229_updated.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= 0.018 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 2 5.49 5 S 35 5.16 5 C 6023 2.51 5 N 1606 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9544 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5427 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 661} Chain: "B" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3981 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 4 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 136 Unusual residues: {'LU9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.44, per 1000 atoms: 0.57 Number of scatterers: 9544 At special positions: 0 Unit cell: (65.32, 76.68, 146.97, 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 35 16.00 P 2 15.00 O 1878 8.00 N 1606 7.00 C 6023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 692 " - pdb=" SG CYS A 698 " 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: 3.87 Conformation dependent library (CDL) restraints added in 1.7 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 16 sheets defined 5.6% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 66 through 72 removed outlier: 5.243A pdb=" N TYR A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 137 through 140 No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 327 through 330 No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.938A pdb=" N ARG B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP B 153 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.078A pdb=" N GLY B 178 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 182 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 588 through 590 No H-bonds generated for 'chain 'B' and resid 588 through 590' Processing sheet with id= A, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.769A pdb=" N VAL A 152 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA A 129 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN A 150 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE A 131 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 148 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 675 through 681 removed outlier: 3.594A pdb=" N LEU A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 307 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 386 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 373 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TRP A 478 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG A 566 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR A 595 " --> pdb=" O ARG A 566 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG A 568 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA A 593 " --> pdb=" O ARG A 568 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A 570 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR A 591 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE A 572 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR A 589 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 574 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A 587 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA A 576 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 585 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 218 through 221 Processing sheet with id= D, first strand: chain 'A' and resid 308 through 314 Processing sheet with id= E, first strand: chain 'A' and resid 526 through 528 Processing sheet with id= F, first strand: chain 'A' and resid 689 through 692 removed outlier: 7.017A pdb=" N PHE A 699 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 63 through 66 Processing sheet with id= H, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.561A pdb=" N GLU B 47 " --> pdb=" O VAL B 315 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= J, first strand: chain 'B' and resid 118 through 126 removed outlier: 3.861A pdb=" N GLN B 158 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 275 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.565A pdb=" N TYR B 300 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= M, first strand: chain 'B' and resid 357 through 360 removed outlier: 5.722A pdb=" N VAL B 422 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLY B 378 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 424 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP B 376 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 546 through 550 removed outlier: 4.517A pdb=" N GLY B 470 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU B 468 " --> pdb=" O ASN B 631 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS B 633 " --> pdb=" O THR B 466 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR B 466 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE B 635 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY B 464 " --> pdb=" O ILE B 635 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 564 through 568 Processing sheet with id= P, first strand: chain 'B' and resid 478 through 483 removed outlier: 3.512A pdb=" N GLY B 478 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B 617 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 613 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE B 560 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N MET B 603 " --> pdb=" O PRO B 558 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASN B 605 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR B 556 " --> pdb=" O ASN B 605 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 4.13 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: 1583 1.31 - 1.43: 2795 1.43 - 1.56: 5308 1.56 - 1.69: 32 1.69 - 1.81: 59 Bond restraints: 9777 Sorted by residual: bond pdb=" C81 LU9 A 801 " pdb=" O81 LU9 A 801 " ideal model delta sigma weight residual 1.185 1.395 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C71 LU9 A 801 " pdb=" O71 LU9 A 801 " ideal model delta sigma weight residual 1.181 1.373 -0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C01 LU9 A 801 " pdb=" O03 LU9 A 801 " ideal model delta sigma weight residual 1.261 1.414 -0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" C01 LU9 A 801 " pdb=" O02 LU9 A 801 " ideal model delta sigma weight residual 1.257 1.402 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C2 LU9 A 801 " pdb=" O05 LU9 A 801 " ideal model delta sigma weight residual 1.362 1.495 -0.133 2.00e-02 2.50e+03 4.44e+01 ... (remaining 9772 not shown) Histogram of bond angle deviations from ideal: 98.71 - 106.26: 269 106.26 - 113.82: 5333 113.82 - 121.38: 4908 121.38 - 128.93: 2712 128.93 - 136.49: 54 Bond angle restraints: 13276 Sorted by residual: angle pdb=" C19 LU9 A 801 " pdb="C110 LU9 A 801 " pdb="C111 LU9 A 801 " ideal model delta sigma weight residual 109.52 136.49 -26.97 3.00e+00 1.11e-01 8.08e+01 angle pdb=" C02 LU9 A 801 " pdb=" C01 LU9 A 801 " pdb=" O02 LU9 A 801 " ideal model delta sigma weight residual 119.95 108.00 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CA PRO A 321 " pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 112.00 106.43 5.57 1.40e+00 5.10e-01 1.58e+01 angle pdb=" C72 LU9 A 801 " pdb=" C71 LU9 A 801 " pdb=" O71 LU9 A 801 " ideal model delta sigma weight residual 119.98 108.95 11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C02 LU9 A 801 " pdb=" C01 LU9 A 801 " pdb=" O03 LU9 A 801 " ideal model delta sigma weight residual 119.93 109.08 10.85 3.00e+00 1.11e-01 1.31e+01 ... (remaining 13271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 5495 34.97 - 69.95: 178 69.95 - 104.92: 30 104.92 - 139.89: 4 139.89 - 174.87: 1 Dihedral angle restraints: 5708 sinusoidal: 2236 harmonic: 3472 Sorted by residual: dihedral pdb=" CA ALA B 186 " pdb=" C ALA B 186 " pdb=" N TRP B 187 " pdb=" CA TRP B 187 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" C58 LU9 A 801 " pdb=" C59 LU9 A 801 " pdb="C510 LU9 A 801 " pdb="C511 LU9 A 801 " ideal model delta sinusoidal sigma weight residual 201.93 27.06 174.87 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C18 LU9 A 801 " pdb=" C19 LU9 A 801 " pdb="C110 LU9 A 801 " pdb="C111 LU9 A 801 " ideal model delta sinusoidal sigma weight residual 184.62 65.70 118.92 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 5705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1129 0.051 - 0.102: 227 0.102 - 0.153: 60 0.153 - 0.203: 1 0.203 - 0.254: 1 Chirality restraints: 1418 Sorted by residual: chirality pdb=" C2 LU9 A 801 " pdb=" C3 LU9 A 801 " pdb=" O05 LU9 A 801 " pdb=" O6 LU9 A 801 " both_signs ideal model delta sigma weight residual False -2.34 -2.60 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB2 LU9 A 801 " pdb=" CB1 LU9 A 801 " pdb=" NB2 LU9 A 801 " pdb=" CB3 LU9 A 801 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CB VAL A 136 " pdb=" CA VAL A 136 " pdb=" CG1 VAL A 136 " pdb=" CG2 VAL A 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1415 not shown) Planarity restraints: 1734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C81 LU9 A 801 " -0.362 2.00e-02 2.50e+03 2.09e-01 4.36e+02 pdb=" C82 LU9 A 801 " 0.112 2.00e-02 2.50e+03 pdb=" O73 LU9 A 801 " 0.124 2.00e-02 2.50e+03 pdb=" O81 LU9 A 801 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" OB3 LU9 A 801 " 0.124 2.00e-02 2.50e+03 2.08e-01 4.33e+02 pdb=" C71 LU9 A 801 " -0.360 2.00e-02 2.50e+03 pdb=" C72 LU9 A 801 " 0.109 2.00e-02 2.50e+03 pdb=" O71 LU9 A 801 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 LU9 A 801 " -0.351 2.00e-02 2.50e+03 2.03e-01 4.11e+02 pdb=" C02 LU9 A 801 " 0.108 2.00e-02 2.50e+03 pdb=" O02 LU9 A 801 " 0.122 2.00e-02 2.50e+03 pdb=" O03 LU9 A 801 " 0.122 2.00e-02 2.50e+03 ... (remaining 1731 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 842 2.74 - 3.28: 9492 3.28 - 3.82: 17075 3.82 - 4.36: 21490 4.36 - 4.90: 38030 Nonbonded interactions: 86929 Sorted by model distance: nonbonded pdb=" O ASN B 238 " pdb=" OG1 THR B 241 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR A 234 " pdb=" OE1 GLN A 236 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR A 243 " pdb=" OE1 GLU A 268 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP A 182 " pdb=" N SER A 183 " model vdw 2.238 2.520 nonbonded pdb=" NE2 GLN B 158 " pdb=" O ASP B 276 " model vdw 2.238 2.520 ... (remaining 86924 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: 4.450 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: 18.780 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.900 Find NCS groups from input model: 0.240 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 0.007 0.210 9777 Z= 0.422 Angle : 0.683 26.969 13276 Z= 0.319 Chirality : 0.044 0.254 1418 Planarity : 0.010 0.209 1734 Dihedral : 18.417 174.868 3518 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.94 % Favored : 93.89 % Rotamer: Outliers : 0.80 % Allowed : 25.50 % Favored : 73.70 % 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: -1.68 (0.24), residues: 1212 helix: -2.24 (0.59), residues: 68 sheet: -1.03 (0.23), residues: 545 loop : -0.91 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 187 HIS 0.002 0.001 HIS A 339 PHE 0.013 0.001 PHE A 115 TYR 0.026 0.001 TYR B 109 ARG 0.001 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.005 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.1619 time to fit residues: 26.5260 Evaluate side-chains 98 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN B 125 GLN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9777 Z= 0.460 Angle : 0.650 12.121 13276 Z= 0.334 Chirality : 0.048 0.163 1418 Planarity : 0.005 0.080 1734 Dihedral : 10.897 113.957 1437 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.33 % Rotamer: Outliers : 4.70 % Allowed : 23.60 % Favored : 71.70 % 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: -1.85 (0.24), residues: 1212 helix: -2.36 (0.56), residues: 67 sheet: -1.12 (0.23), residues: 529 loop : -1.07 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 187 HIS 0.006 0.001 HIS A 339 PHE 0.018 0.002 PHE B 256 TYR 0.022 0.002 TYR A 325 ARG 0.002 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 98 time to evaluate : 1.468 Fit side-chains REVERT: A 379 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7926 (t70) REVERT: B 544 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8057 (mtmm) outliers start: 47 outliers final: 26 residues processed: 134 average time/residue: 0.1627 time to fit residues: 35.0212 Evaluate side-chains 120 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 109 optimal weight: 0.0040 chunk 37 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 114 ASN A 385 ASN A 427 ASN A 675 ASN B 125 GLN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9777 Z= 0.197 Angle : 0.544 10.567 13276 Z= 0.278 Chirality : 0.045 0.146 1418 Planarity : 0.004 0.067 1734 Dihedral : 9.687 102.572 1433 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.39 % Rotamer: Outliers : 4.30 % Allowed : 24.40 % Favored : 71.30 % 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: -1.85 (0.24), residues: 1212 helix: -2.27 (0.58), residues: 67 sheet: -1.12 (0.23), residues: 518 loop : -1.09 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 187 HIS 0.003 0.001 HIS A 679 PHE 0.016 0.001 PHE B 256 TYR 0.017 0.001 TYR A 325 ARG 0.001 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 1.129 Fit side-chains REVERT: A 399 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8720 (mt) REVERT: B 401 THR cc_start: 0.8671 (m) cc_final: 0.8211 (p) REVERT: B 509 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7648 (pp) REVERT: B 544 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8029 (mtmm) REVERT: B 625 MET cc_start: 0.8382 (ptt) cc_final: 0.8179 (ptt) outliers start: 43 outliers final: 23 residues processed: 137 average time/residue: 0.1800 time to fit residues: 39.9688 Evaluate side-chains 125 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 0.0370 chunk 104 optimal weight: 0.0000 chunk 31 optimal weight: 0.0470 chunk 97 optimal weight: 4.9990 overall best weight: 0.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9777 Z= 0.163 Angle : 0.516 9.785 13276 Z= 0.262 Chirality : 0.044 0.150 1418 Planarity : 0.004 0.058 1734 Dihedral : 8.820 101.290 1433 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.53 % Favored : 94.31 % Rotamer: Outliers : 4.70 % Allowed : 23.90 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.24), residues: 1212 helix: -2.22 (0.58), residues: 67 sheet: -1.14 (0.23), residues: 509 loop : -0.93 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 187 HIS 0.002 0.001 HIS A 288 PHE 0.016 0.001 PHE B 256 TYR 0.015 0.001 TYR A 325 ARG 0.002 0.000 ARG B 535 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 103 time to evaluate : 1.137 Fit side-chains REVERT: A 399 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 401 THR cc_start: 0.8685 (m) cc_final: 0.8244 (p) REVERT: B 458 ARG cc_start: 0.5670 (OUTLIER) cc_final: 0.5269 (ptp90) REVERT: B 509 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7596 (pp) REVERT: B 544 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7928 (mtmm) REVERT: B 625 MET cc_start: 0.8370 (ptt) cc_final: 0.8083 (ptt) outliers start: 47 outliers final: 32 residues processed: 142 average time/residue: 0.1705 time to fit residues: 37.3153 Evaluate side-chains 135 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN A 385 ASN A 675 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 578 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 9777 Z= 0.507 Angle : 0.662 12.675 13276 Z= 0.339 Chirality : 0.048 0.145 1418 Planarity : 0.005 0.056 1734 Dihedral : 9.234 101.040 1433 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 5.30 % Allowed : 24.40 % Favored : 70.30 % 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: -1.96 (0.23), residues: 1212 helix: -2.52 (0.55), residues: 70 sheet: -1.20 (0.23), residues: 507 loop : -1.13 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 283 HIS 0.008 0.001 HIS A 679 PHE 0.016 0.002 PHE B 256 TYR 0.024 0.002 TYR A 325 ARG 0.007 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 93 time to evaluate : 1.492 Fit side-chains REVERT: A 379 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7912 (t70) REVERT: B 192 TYR cc_start: 0.8594 (m-80) cc_final: 0.8370 (m-80) REVERT: B 458 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5401 (ttp-110) REVERT: B 509 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7739 (pp) REVERT: B 637 GLN cc_start: 0.8423 (tp40) cc_final: 0.8117 (tp40) outliers start: 53 outliers final: 42 residues processed: 141 average time/residue: 0.1661 time to fit residues: 36.8651 Evaluate side-chains 136 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 91 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 462 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9777 Z= 0.237 Angle : 0.560 10.793 13276 Z= 0.285 Chirality : 0.045 0.146 1418 Planarity : 0.004 0.056 1734 Dihedral : 8.954 101.875 1433 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.36 % Favored : 94.47 % Rotamer: Outliers : 5.10 % Allowed : 24.70 % Favored : 70.20 % 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: -1.94 (0.24), residues: 1212 helix: -2.40 (0.57), residues: 68 sheet: -1.23 (0.23), residues: 519 loop : -1.08 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 187 HIS 0.004 0.001 HIS A 679 PHE 0.016 0.001 PHE B 256 TYR 0.018 0.001 TYR A 325 ARG 0.005 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 101 time to evaluate : 1.035 Fit side-chains REVERT: A 379 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7816 (t70) REVERT: A 399 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8753 (mt) REVERT: B 192 TYR cc_start: 0.8432 (m-80) cc_final: 0.8214 (m-80) REVERT: B 401 THR cc_start: 0.8690 (m) cc_final: 0.8242 (p) REVERT: B 458 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5336 (ttp-110) REVERT: B 509 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7654 (pp) REVERT: B 625 MET cc_start: 0.8395 (ptt) cc_final: 0.8130 (ptt) outliers start: 51 outliers final: 41 residues processed: 143 average time/residue: 0.1476 time to fit residues: 33.8752 Evaluate side-chains 139 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 94 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 116 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 578 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9777 Z= 0.201 Angle : 0.534 10.285 13276 Z= 0.271 Chirality : 0.044 0.145 1418 Planarity : 0.004 0.055 1734 Dihedral : 8.656 101.198 1433 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.19 % Favored : 93.65 % Rotamer: Outliers : 5.10 % Allowed : 24.80 % Favored : 70.10 % 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: -1.82 (0.24), residues: 1212 helix: -2.32 (0.58), residues: 68 sheet: -1.20 (0.22), residues: 540 loop : -0.91 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 187 HIS 0.004 0.001 HIS A 679 PHE 0.014 0.001 PHE B 256 TYR 0.017 0.001 TYR A 325 ARG 0.003 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 100 time to evaluate : 0.987 Fit side-chains REVERT: A 379 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7729 (t70) REVERT: A 399 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 401 THR cc_start: 0.8672 (m) cc_final: 0.8228 (p) REVERT: B 458 ARG cc_start: 0.5744 (OUTLIER) cc_final: 0.5338 (ptp90) REVERT: B 509 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7613 (pp) REVERT: B 625 MET cc_start: 0.8396 (ptt) cc_final: 0.8175 (ptt) REVERT: B 637 GLN cc_start: 0.8388 (tp40) cc_final: 0.8096 (tp40) outliers start: 51 outliers final: 43 residues processed: 145 average time/residue: 0.1554 time to fit residues: 35.6967 Evaluate side-chains 144 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 97 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 0.0570 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.0020 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.5308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9777 Z= 0.198 Angle : 0.538 10.244 13276 Z= 0.272 Chirality : 0.044 0.145 1418 Planarity : 0.004 0.055 1734 Dihedral : 8.585 100.929 1433 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.61 % Favored : 94.22 % Rotamer: Outliers : 5.40 % Allowed : 25.20 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.24), residues: 1212 helix: -2.28 (0.58), residues: 68 sheet: -1.18 (0.22), residues: 540 loop : -0.91 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 187 HIS 0.004 0.001 HIS A 679 PHE 0.014 0.001 PHE B 256 TYR 0.016 0.001 TYR A 325 ARG 0.004 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 98 time to evaluate : 1.166 Fit side-chains REVERT: A 399 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8671 (mt) REVERT: B 401 THR cc_start: 0.8651 (m) cc_final: 0.8211 (p) REVERT: B 458 ARG cc_start: 0.5641 (OUTLIER) cc_final: 0.5278 (ptp90) REVERT: B 509 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7589 (pp) REVERT: B 625 MET cc_start: 0.8409 (ptt) cc_final: 0.8156 (ptt) outliers start: 54 outliers final: 47 residues processed: 144 average time/residue: 0.1558 time to fit residues: 35.9022 Evaluate side-chains 146 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 96 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9777 Z= 0.236 Angle : 0.546 10.504 13276 Z= 0.276 Chirality : 0.045 0.145 1418 Planarity : 0.004 0.055 1734 Dihedral : 8.571 100.663 1433 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.27 % Favored : 93.56 % Rotamer: Outliers : 5.20 % Allowed : 25.50 % Favored : 69.30 % 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: -1.78 (0.24), residues: 1212 helix: -2.28 (0.58), residues: 68 sheet: -1.15 (0.22), residues: 535 loop : -0.93 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 221 HIS 0.004 0.001 HIS A 679 PHE 0.013 0.001 PHE B 256 TYR 0.017 0.001 TYR A 325 ARG 0.004 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 96 time to evaluate : 1.108 Fit side-chains REVERT: A 399 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8680 (mt) REVERT: B 401 THR cc_start: 0.8660 (m) cc_final: 0.8214 (p) REVERT: B 458 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.5304 (ptp90) REVERT: B 509 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7614 (pp) REVERT: B 625 MET cc_start: 0.8436 (ptt) cc_final: 0.8225 (ptt) outliers start: 52 outliers final: 48 residues processed: 142 average time/residue: 0.1537 time to fit residues: 35.0559 Evaluate side-chains 146 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 95 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 ARG Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.0670 chunk 120 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 74 optimal weight: 0.0870 chunk 58 optimal weight: 0.0170 chunk 76 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9777 Z= 0.145 Angle : 0.521 9.387 13276 Z= 0.263 Chirality : 0.044 0.141 1418 Planarity : 0.004 0.055 1734 Dihedral : 8.375 100.425 1433 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 4.50 % Allowed : 26.10 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1212 helix: -2.29 (0.62), residues: 62 sheet: -1.12 (0.22), residues: 525 loop : -0.80 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 221 HIS 0.002 0.001 HIS B 209 PHE 0.012 0.001 PHE B 256 TYR 0.014 0.001 TYR A 325 ARG 0.004 0.000 ARG B 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 100 time to evaluate : 1.015 Fit side-chains REVERT: A 399 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8562 (mt) REVERT: B 401 THR cc_start: 0.8671 (m) cc_final: 0.8219 (p) REVERT: B 509 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7573 (pp) REVERT: B 625 MET cc_start: 0.8404 (ptt) cc_final: 0.8178 (ptt) outliers start: 45 outliers final: 33 residues processed: 139 average time/residue: 0.1536 time to fit residues: 34.0366 Evaluate side-chains 131 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 96 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 499 CYS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 616 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122501 restraints weight = 10768.386| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.60 r_work: 0.3333 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9777 Z= 0.373 Angle : 0.605 10.466 13276 Z= 0.308 Chirality : 0.047 0.149 1418 Planarity : 0.004 0.055 1734 Dihedral : 8.656 100.505 1433 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.44 % Favored : 93.40 % Rotamer: Outliers : 4.00 % Allowed : 26.70 % Favored : 69.30 % 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: -1.89 (0.24), residues: 1212 helix: -2.39 (0.56), residues: 68 sheet: -1.26 (0.22), residues: 530 loop : -0.96 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 283 HIS 0.006 0.001 HIS A 679 PHE 0.016 0.001 PHE B 256 TYR 0.017 0.002 TYR A 325 ARG 0.003 0.000 ARG B 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.74 seconds wall clock time: 45 minutes 51.18 seconds (2751.18 seconds total)