Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 11:44:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/04_2023/8a8c_15229_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/04_2023/8a8c_15229.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/04_2023/8a8c_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_15229/04_2023/8a8c_15229_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/04_2023/8a8c_15229_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/04_2023/8a8c_15229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/04_2023/8a8c_15229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/04_2023/8a8c_15229_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8c_15229/04_2023/8a8c_15229_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 5.52, per 1000 atoms: 0.58 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: 4.13 Conformation dependent library (CDL) restraints added in 1.5 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: 1.46 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: 3.76 Time building geometry restraints manager: 4.42 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: 5470 34.97 - 69.95: 170 69.95 - 104.92: 27 104.92 - 139.89: 3 139.89 - 174.87: 1 Dihedral angle restraints: 5671 sinusoidal: 2199 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 5668 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: 5.950 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: 17.920 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.530 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.650 ------------------------------------------------------------------------------- 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 : 18.088 174.868 3481 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 % 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 *********************** 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 : 1.129 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.1656 time to fit residues: 27.3136 Evaluate side-chains 98 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0929 time to fit residues: 2.3346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.8432 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 9777 Z= 0.462 Angle : 0.649 12.100 13276 Z= 0.335 Chirality : 0.048 0.163 1418 Planarity : 0.005 0.080 1734 Dihedral : 9.396 115.733 1393 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.33 % Rotamer Outliers : 4.40 % 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: -1.87 (0.24), residues: 1212 helix: -2.34 (0.56), residues: 67 sheet: -1.09 (0.23), residues: 517 loop : -1.13 (0.24), residues: 628 *********************** 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 143 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 99 time to evaluate : 1.191 Fit side-chains outliers start: 44 outliers final: 25 residues processed: 133 average time/residue: 0.1560 time to fit residues: 33.1862 Evaluate side-chains 118 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0976 time to fit residues: 5.9485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 109 optimal weight: 0.0060 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0980 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= 0.210 Angle : 0.545 10.666 13276 Z= 0.279 Chirality : 0.045 0.150 1418 Planarity : 0.004 0.066 1734 Dihedral : 8.244 89.440 1393 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.36 % Favored : 94.47 % Rotamer Outliers : 3.30 % 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: -1.87 (0.24), residues: 1212 helix: -2.31 (0.58), residues: 67 sheet: -1.14 (0.23), residues: 518 loop : -1.08 (0.24), residues: 627 *********************** 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 137 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.078 Fit side-chains outliers start: 33 outliers final: 11 residues processed: 128 average time/residue: 0.1509 time to fit residues: 31.3462 Evaluate side-chains 109 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0923 time to fit residues: 3.4581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 104 optimal weight: 0.0270 chunk 31 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.1097 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= 0.201 Angle : 0.538 10.341 13276 Z= 0.272 Chirality : 0.045 0.155 1418 Planarity : 0.004 0.058 1734 Dihedral : 7.609 89.053 1393 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.02 % Favored : 93.81 % Rotamer Outliers : 2.60 % 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: -1.77 (0.24), residues: 1212 helix: -2.31 (0.57), residues: 68 sheet: -1.08 (0.23), residues: 509 loop : -1.02 (0.24), residues: 635 *********************** 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 129 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 1.169 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 127 average time/residue: 0.1665 time to fit residues: 33.6503 Evaluate side-chains 112 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0974 time to fit residues: 4.6157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 9777 Z= 0.324 Angle : 0.581 11.338 13276 Z= 0.294 Chirality : 0.046 0.142 1418 Planarity : 0.004 0.057 1734 Dihedral : 7.520 89.118 1393 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.60 % Favored : 93.23 % Rotamer Outliers : 1.20 % 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: -1.84 (0.24), residues: 1212 helix: -2.33 (0.57), residues: 68 sheet: -1.16 (0.23), residues: 509 loop : -1.03 (0.24), residues: 635 *********************** 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 108 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.077 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 105 average time/residue: 0.1547 time to fit residues: 26.4380 Evaluate side-chains 103 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0925 time to fit residues: 3.1127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9777 Z= 0.291 Angle : 0.567 10.983 13276 Z= 0.287 Chirality : 0.046 0.149 1418 Planarity : 0.004 0.057 1734 Dihedral : 7.414 87.774 1393 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.52 % Favored : 93.32 % Rotamer Outliers : 2.00 % 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: -1.87 (0.23), residues: 1212 helix: -2.34 (0.57), residues: 68 sheet: -1.21 (0.23), residues: 509 loop : -1.03 (0.24), residues: 635 *********************** 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 118 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.263 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 112 average time/residue: 0.1654 time to fit residues: 30.0170 Evaluate side-chains 99 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1064 time to fit residues: 3.3796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 85 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9777 Z= 0.239 Angle : 0.556 10.637 13276 Z= 0.280 Chirality : 0.045 0.147 1418 Planarity : 0.004 0.059 1734 Dihedral : 7.280 89.841 1393 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.52 % Favored : 93.32 % Rotamer Outliers : 1.10 % 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: -1.83 (0.24), residues: 1212 helix: -2.30 (0.58), residues: 68 sheet: -1.25 (0.22), residues: 530 loop : -0.90 (0.25), residues: 614 *********************** 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 106 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.066 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 103 average time/residue: 0.1611 time to fit residues: 27.1219 Evaluate side-chains 99 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1061 time to fit residues: 2.8948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 79 optimal weight: 0.0170 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 overall best weight: 0.8822 ------------------------------------------------------------------------------- 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 675 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9777 Z= 0.272 Angle : 0.567 10.982 13276 Z= 0.287 Chirality : 0.045 0.149 1418 Planarity : 0.004 0.058 1734 Dihedral : 7.223 88.343 1393 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.44 % Favored : 93.40 % Rotamer Outliers : 1.10 % 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: -1.88 (0.23), residues: 1212 helix: -2.32 (0.58), residues: 68 sheet: -1.23 (0.22), residues: 509 loop : -1.02 (0.24), residues: 635 *********************** 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 104 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.110 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.1623 time to fit residues: 27.0530 Evaluate side-chains 97 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1143 time to fit residues: 2.7043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 114 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9777 Z= 0.204 Angle : 0.545 10.322 13276 Z= 0.275 Chirality : 0.045 0.145 1418 Planarity : 0.004 0.058 1734 Dihedral : 7.104 86.920 1393 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.94 % Favored : 93.89 % Rotamer Outliers : 0.40 % 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: -1.78 (0.24), residues: 1212 helix: -2.32 (0.62), residues: 62 sheet: -1.21 (0.22), residues: 530 loop : -0.88 (0.25), residues: 620 *********************** 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 98 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.096 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 0.1630 time to fit residues: 25.9482 Evaluate side-chains 96 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0982 time to fit residues: 2.1847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 0.0670 chunk 120 optimal weight: 0.0000 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.3722 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9777 Z= 0.164 Angle : 0.525 9.659 13276 Z= 0.265 Chirality : 0.044 0.143 1418 Planarity : 0.004 0.059 1734 Dihedral : 6.899 88.088 1393 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.39 % Rotamer Outliers : 0.30 % 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: -1.70 (0.24), residues: 1212 helix: -2.27 (0.62), residues: 61 sheet: -1.13 (0.22), residues: 530 loop : -0.85 (0.25), residues: 621 ********************** 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 104 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.014 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 103 average time/residue: 0.1693 time to fit residues: 27.4823 Evaluate side-chains 97 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0891 time to fit residues: 1.8097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 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: 1.5788 ------------------------------------------------------------------------------- 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 ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120997 restraints weight = 10813.072| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.60 r_work: 0.3309 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 9777 Z= 0.436 Angle : 0.647 11.937 13276 Z= 0.329 Chirality : 0.048 0.154 1418 Planarity : 0.004 0.058 1734 Dihedral : 7.196 83.209 1393 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.93 % Favored : 92.90 % Rotamer Outliers : 0.60 % 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: -1.98 (0.23), residues: 1212 helix: -2.49 (0.55), residues: 70 sheet: -1.30 (0.22), residues: 511 loop : -1.06 (0.24), residues: 631 =============================================================================== Job complete usr+sys time: 2215.57 seconds wall clock time: 41 minutes 25.17 seconds (2485.17 seconds total)