Starting phenix.real_space_refine on Thu Feb 15 18:49:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/02_2024/7ytj_34090_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/02_2024/7ytj_34090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/02_2024/7ytj_34090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/02_2024/7ytj_34090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/02_2024/7ytj_34090_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/02_2024/7ytj_34090_updated.pdb" } resolution = 3.0 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= 0.002 sd= 0.089 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 22 5.49 5 S 34 5.16 5 C 8474 2.51 5 N 2194 2.21 5 O 2413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 24": "OD1" <-> "OD2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D ASP 473": "OD1" <-> "OD2" Residue "D PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ASP 478": "OD1" <-> "OD2" Residue "E ASP 481": "OD1" <-> "OD2" Residue "E ASP 496": "OD1" <-> "OD2" Residue "E GLU 550": "OE1" <-> "OE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 585": "OD1" <-> "OD2" Residue "E GLU 733": "OE1" <-> "OE2" Residue "E PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13137 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 4940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4940 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 574} Chain breaks: 2 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 941 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 811 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 811 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "E" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5408 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 28, 'TRANS': 621} Chain breaks: 3 Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 172 Unusual residues: {'IHP': 3, 'PC1': 1, 'PO4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.30, per 1000 atoms: 0.56 Number of scatterers: 13137 At special positions: 0 Unit cell: (111.28, 93.09, 169.06, 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 34 16.00 P 22 15.00 O 2413 8.00 N 2194 7.00 C 8474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.32 Conformation dependent library (CDL) restraints added in 2.2 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 4 sheets defined 57.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'D' and resid 4 through 10 Processing helix chain 'D' and resid 23 through 36 Processing helix chain 'D' and resid 43 through 90 removed outlier: 3.580A pdb=" N LEU D 89 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP D 90 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 138 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 162 through 179 Processing helix chain 'D' and resid 206 through 218 removed outlier: 4.870A pdb=" N THR D 210 " --> pdb=" O ASP D 207 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU D 211 " --> pdb=" O ASN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 302 through 310 removed outlier: 4.802A pdb=" N ASN D 306 " --> pdb=" O ARG D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 318 No H-bonds generated for 'chain 'D' and resid 315 through 318' Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'D' and resid 330 through 350 Processing helix chain 'D' and resid 440 through 446 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 479 through 481 No H-bonds generated for 'chain 'D' and resid 479 through 481' Processing helix chain 'D' and resid 622 through 651 removed outlier: 3.998A pdb=" N PHE D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU D 629 " --> pdb=" O TYR D 625 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 632 " --> pdb=" O THR D 628 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE D 638 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 689 removed outlier: 3.754A pdb=" N GLY D 663 " --> pdb=" O ILE D 659 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 688 " --> pdb=" O VAL D 684 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS D 689 " --> pdb=" O ASN D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 723 Processing helix chain 'A' and resid 57 through 87 Processing helix chain 'A' and resid 90 through 123 removed outlier: 4.147A pdb=" N GLY A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 Processing helix chain 'B' and resid 57 through 87 removed outlier: 3.673A pdb=" N PHE B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 123 Processing helix chain 'B' and resid 133 through 155 Processing helix chain 'C' and resid 58 through 87 removed outlier: 3.533A pdb=" N PHE C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 123 Processing helix chain 'C' and resid 131 through 155 Proline residue: C 135 - end of helix Processing helix chain 'E' and resid 33 through 38 Processing helix chain 'E' and resid 42 through 47 removed outlier: 5.267A pdb=" N ASP E 46 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 63 removed outlier: 4.430A pdb=" N SER E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 113 removed outlier: 4.616A pdb=" N ASN E 113 " --> pdb=" O ASP E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 125 through 163 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 243 through 254 removed outlier: 4.427A pdb=" N MET E 247 " --> pdb=" O ASP E 243 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 395 through 399 Processing helix chain 'E' and resid 405 through 416 Processing helix chain 'E' and resid 421 through 441 Processing helix chain 'E' and resid 504 through 507 Processing helix chain 'E' and resid 537 through 543 Processing helix chain 'E' and resid 556 through 565 Processing helix chain 'E' and resid 579 through 581 No H-bonds generated for 'chain 'E' and resid 579 through 581' Processing helix chain 'E' and resid 592 through 594 No H-bonds generated for 'chain 'E' and resid 592 through 594' Processing helix chain 'E' and resid 597 through 617 Processing helix chain 'E' and resid 723 through 754 Processing helix chain 'E' and resid 763 through 796 Processing helix chain 'E' and resid 806 through 828 Processing helix chain 'E' and resid 830 through 832 No H-bonds generated for 'chain 'E' and resid 830 through 832' Processing sheet with id= A, first strand: chain 'D' and resid 196 through 204 Processing sheet with id= B, first strand: chain 'D' and resid 290 through 301 removed outlier: 7.208A pdb=" N THR D 276 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR D 269 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 261 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS D 264 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 356 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP D 244 " --> pdb=" O PRO D 354 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 233 through 241 Processing sheet with id= D, first strand: chain 'E' and resid 383 through 390 removed outlier: 4.207A pdb=" N ILE E 365 " --> pdb=" O MET E 390 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU E 351 " --> pdb=" O PHE E 330 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP E 331 " --> pdb=" O PRO E 445 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2280 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: 3.70 Time building geometry restraints manager: 5.70 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: 2082 1.31 - 1.44: 3642 1.44 - 1.56: 7624 1.56 - 1.69: 25 1.69 - 1.82: 59 Bond restraints: 13432 Sorted by residual: bond pdb=" C21 PC1 E 901 " pdb=" O21 PC1 E 901 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C31 PC1 E 901 " pdb=" O31 PC1 E 901 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C31 PC1 D1003 " pdb=" O31 PC1 D1003 " ideal model delta sigma weight residual 1.330 1.397 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C21 PC1 D1003 " pdb=" O21 PC1 D1003 " ideal model delta sigma weight residual 1.331 1.396 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O3 PO4 D1005 " pdb=" P PO4 D1005 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.94e+00 ... (remaining 13427 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.92: 214 104.92 - 112.18: 6853 112.18 - 119.45: 4326 119.45 - 126.72: 6610 126.72 - 133.98: 180 Bond angle restraints: 18183 Sorted by residual: angle pdb=" CA PRO E 502 " pdb=" N PRO E 502 " pdb=" CD PRO E 502 " ideal model delta sigma weight residual 112.00 98.48 13.52 1.40e+00 5.10e-01 9.33e+01 angle pdb=" CA PRO E 168 " pdb=" N PRO E 168 " pdb=" CD PRO E 168 " ideal model delta sigma weight residual 112.00 100.68 11.32 1.40e+00 5.10e-01 6.54e+01 angle pdb=" O12 PC1 E 901 " pdb=" P PC1 E 901 " pdb=" O14 PC1 E 901 " ideal model delta sigma weight residual 123.67 109.24 14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" O12 PC1 D1003 " pdb=" P PC1 D1003 " pdb=" O14 PC1 D1003 " ideal model delta sigma weight residual 123.67 109.48 14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" CA LEU E 57 " pdb=" CB LEU E 57 " pdb=" CG LEU E 57 " ideal model delta sigma weight residual 116.30 130.72 -14.42 3.50e+00 8.16e-02 1.70e+01 ... (remaining 18178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 7795 35.66 - 71.32: 312 71.32 - 106.98: 18 106.98 - 142.63: 18 142.63 - 178.29: 3 Dihedral angle restraints: 8146 sinusoidal: 3520 harmonic: 4626 Sorted by residual: dihedral pdb=" C4 IHP D1001 " pdb=" C2 IHP D1001 " pdb=" C3 IHP D1001 " pdb=" O12 IHP D1001 " ideal model delta sinusoidal sigma weight residual 60.90 -117.39 178.29 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O12 IHP D1001 " pdb=" C2 IHP D1001 " pdb=" C3 IHP D1001 " pdb=" O13 IHP D1001 " ideal model delta sinusoidal sigma weight residual 64.08 -121.46 -174.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C6 IHP D1004 " pdb=" C1 IHP D1004 " pdb=" C2 IHP D1004 " pdb=" O12 IHP D1004 " ideal model delta sinusoidal sigma weight residual 61.05 -153.70 -145.25 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 8143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.044: 1992 1.044 - 2.088: 0 2.088 - 3.132: 0 3.132 - 4.176: 0 4.176 - 5.221: 9 Chirality restraints: 2001 Sorted by residual: chirality pdb=" C4 IHP D1002 " pdb=" C3 IHP D1002 " pdb=" C5 IHP D1002 " pdb=" O14 IHP D1002 " both_signs ideal model delta sigma weight residual False 2.48 -2.74 5.22 2.00e-01 2.50e+01 6.81e+02 chirality pdb=" C4 IHP D1004 " pdb=" C3 IHP D1004 " pdb=" C5 IHP D1004 " pdb=" O14 IHP D1004 " both_signs ideal model delta sigma weight residual False 2.48 -2.66 5.14 2.00e-01 2.50e+01 6.61e+02 chirality pdb=" C1 IHP D1002 " pdb=" C2 IHP D1002 " pdb=" C6 IHP D1002 " pdb=" O11 IHP D1002 " both_signs ideal model delta sigma weight residual False 2.32 -2.74 5.06 2.00e-01 2.50e+01 6.39e+02 ... (remaining 1998 not shown) Planarity restraints: 2267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 167 " -0.095 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO E 168 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 501 " 0.084 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO E 502 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO E 502 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 502 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 56 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 57 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.033 5.00e-02 4.00e+02 ... (remaining 2264 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1176 2.74 - 3.28: 12951 3.28 - 3.82: 22581 3.82 - 4.36: 25810 4.36 - 4.90: 45327 Nonbonded interactions: 107845 Sorted by model distance: nonbonded pdb=" OH TYR E 409 " pdb=" O45 IHP D1004 " model vdw 2.203 2.440 nonbonded pdb=" OE2 GLU E 90 " pdb=" OG1 THR E 94 " model vdw 2.245 2.440 nonbonded pdb=" O PRO D 95 " pdb=" OG1 THR D 96 " model vdw 2.253 2.440 nonbonded pdb=" O GLY D 644 " pdb=" OG1 THR D 648 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR D 23 " pdb=" O32 IHP D1001 " model vdw 2.288 2.440 ... (remaining 107840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 156) selection = chain 'B' selection = chain 'C' } 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: 0.900 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: 0.020 Extract box with map and model: 5.240 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.530 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 13432 Z= 0.278 Angle : 0.812 14.426 18183 Z= 0.373 Chirality : 0.332 5.221 2001 Planarity : 0.006 0.135 2267 Dihedral : 18.798 178.292 5150 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.41 % Allowed : 19.31 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.69 (0.22), residues: 1554 helix: 2.06 (0.17), residues: 920 sheet: 0.41 (0.38), residues: 180 loop : -0.51 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 268 HIS 0.002 0.001 HIS E 160 PHE 0.029 0.002 PHE E 183 TYR 0.026 0.001 TYR E 198 ARG 0.012 0.000 ARG D 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 9 SER cc_start: 0.7566 (m) cc_final: 0.7326 (t) REVERT: D 383 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7695 (mtt) REVERT: D 443 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7705 (mtm180) REVERT: E 112 GLU cc_start: 0.7764 (pp20) cc_final: 0.7509 (pp20) REVERT: E 189 TYR cc_start: 0.7870 (m-80) cc_final: 0.7569 (m-80) REVERT: E 533 MET cc_start: 0.2802 (tpp) cc_final: 0.2522 (tpp) REVERT: E 573 ASN cc_start: 0.8132 (p0) cc_final: 0.7905 (p0) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 1.0153 time to fit residues: 180.3439 Evaluate side-chains 145 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.3980 chunk 141 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 160 ASN D 198 GLN D 264 HIS D 335 ASN D 427 ASN D 605 GLN E 101 ASN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 ASN E 462 GLN E 527 ASN E 602 GLN ** E 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13432 Z= 0.188 Angle : 0.585 10.667 18183 Z= 0.275 Chirality : 0.042 0.474 2001 Planarity : 0.004 0.047 2267 Dihedral : 12.371 107.954 1979 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.17 % Allowed : 16.42 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.95 (0.22), residues: 1554 helix: 2.29 (0.17), residues: 921 sheet: 0.42 (0.39), residues: 178 loop : -0.41 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 268 HIS 0.003 0.001 HIS E 256 PHE 0.020 0.001 PHE E 145 TYR 0.034 0.001 TYR E 198 ARG 0.004 0.000 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7316 (tp30) cc_final: 0.6968 (tp30) REVERT: D 383 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7523 (mtt) REVERT: D 440 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: A 85 LEU cc_start: 0.8119 (tp) cc_final: 0.7871 (tp) REVERT: C 122 ARG cc_start: 0.6074 (mpt180) cc_final: 0.5777 (mmp-170) REVERT: E 112 GLU cc_start: 0.7789 (pp20) cc_final: 0.7509 (pp20) REVERT: E 189 TYR cc_start: 0.7822 (m-80) cc_final: 0.7535 (m-80) REVERT: E 533 MET cc_start: 0.2784 (tpp) cc_final: 0.2547 (tpp) REVERT: E 573 ASN cc_start: 0.8089 (p0) cc_final: 0.7873 (p0) outliers start: 45 outliers final: 19 residues processed: 175 average time/residue: 1.0728 time to fit residues: 208.3669 Evaluate side-chains 153 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 693 ASP Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 753 ILE Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.0170 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 96 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 48 optimal weight: 0.0040 chunk 113 optimal weight: 20.0000 overall best weight: 0.4832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 160 ASN D 335 ASN ** E 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13432 Z= 0.164 Angle : 0.533 13.889 18183 Z= 0.257 Chirality : 0.040 0.305 2001 Planarity : 0.004 0.054 2267 Dihedral : 11.715 105.655 1959 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.40 % Allowed : 17.27 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.22), residues: 1554 helix: 2.36 (0.17), residues: 925 sheet: 0.44 (0.39), residues: 178 loop : -0.38 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 268 HIS 0.002 0.000 HIS E 256 PHE 0.020 0.001 PHE B 140 TYR 0.023 0.001 TYR E 198 ARG 0.009 0.000 ARG D 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: D 51 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6719 (mt-10) REVERT: D 163 GLU cc_start: 0.7356 (tp30) cc_final: 0.6958 (tp30) REVERT: D 200 THR cc_start: 0.8347 (m) cc_final: 0.8141 (p) REVERT: D 383 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7303 (mtt) REVERT: D 440 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: D 712 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6803 (mp) REVERT: A 85 LEU cc_start: 0.8110 (tp) cc_final: 0.7849 (tp) REVERT: B 140 PHE cc_start: 0.7703 (t80) cc_final: 0.6975 (t80) REVERT: C 101 PHE cc_start: 0.7342 (t80) cc_final: 0.7138 (t80) REVERT: C 122 ARG cc_start: 0.6113 (mpt180) cc_final: 0.5825 (mmp-170) REVERT: E 95 PHE cc_start: 0.7925 (t80) cc_final: 0.7674 (t80) REVERT: E 112 GLU cc_start: 0.7524 (pp20) cc_final: 0.7178 (pp20) REVERT: E 189 TYR cc_start: 0.7761 (m-80) cc_final: 0.7472 (m-80) REVERT: E 268 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5730 (tp30) REVERT: E 533 MET cc_start: 0.2957 (tpp) cc_final: 0.2728 (tpp) outliers start: 34 outliers final: 16 residues processed: 169 average time/residue: 0.9996 time to fit residues: 189.0755 Evaluate side-chains 152 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 693 ASP Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 74 optimal weight: 0.0870 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN A 149 ASN E 844 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13432 Z= 0.183 Angle : 0.514 9.369 18183 Z= 0.253 Chirality : 0.039 0.287 2001 Planarity : 0.004 0.102 2267 Dihedral : 11.436 104.128 1957 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.45 % Allowed : 16.35 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.22), residues: 1554 helix: 2.43 (0.17), residues: 922 sheet: 0.46 (0.38), residues: 178 loop : -0.37 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 268 HIS 0.002 0.001 HIS E 256 PHE 0.017 0.001 PHE E 95 TYR 0.022 0.001 TYR D 679 ARG 0.017 0.000 ARG E 738 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 140 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: D 51 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6717 (mt-10) REVERT: D 163 GLU cc_start: 0.7428 (tp30) cc_final: 0.6986 (tp30) REVERT: D 383 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8293 (mpt) REVERT: D 440 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: D 712 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6846 (mp) REVERT: A 85 LEU cc_start: 0.8154 (tp) cc_final: 0.7885 (tp) REVERT: C 122 ARG cc_start: 0.6178 (mpt180) cc_final: 0.5922 (mmp-170) REVERT: E 112 GLU cc_start: 0.7554 (pp20) cc_final: 0.7170 (pp20) REVERT: E 189 TYR cc_start: 0.7775 (m-80) cc_final: 0.7464 (m-80) REVERT: E 268 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5735 (tp30) outliers start: 49 outliers final: 21 residues processed: 175 average time/residue: 0.9728 time to fit residues: 191.1201 Evaluate side-chains 156 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 693 ASP Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13432 Z= 0.257 Angle : 0.563 13.631 18183 Z= 0.275 Chirality : 0.041 0.345 2001 Planarity : 0.004 0.047 2267 Dihedral : 11.326 102.835 1957 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.24 % Allowed : 17.05 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.99 (0.22), residues: 1554 helix: 2.30 (0.17), residues: 929 sheet: 0.48 (0.39), residues: 178 loop : -0.43 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 268 HIS 0.003 0.001 HIS E 256 PHE 0.023 0.002 PHE B 140 TYR 0.034 0.001 TYR D 679 ARG 0.007 0.000 ARG E 738 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 146 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: D 51 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6805 (mt-10) REVERT: D 163 GLU cc_start: 0.7447 (tp30) cc_final: 0.7005 (tp30) REVERT: D 440 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: D 712 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7055 (mp) REVERT: A 44 THR cc_start: 0.6721 (OUTLIER) cc_final: 0.6481 (p) REVERT: B 140 PHE cc_start: 0.7675 (t80) cc_final: 0.7033 (t80) REVERT: C 101 PHE cc_start: 0.7403 (t80) cc_final: 0.7136 (t80) REVERT: C 122 ARG cc_start: 0.6222 (mpt180) cc_final: 0.5958 (mmp-170) REVERT: E 112 GLU cc_start: 0.7499 (pp20) cc_final: 0.7089 (pp20) REVERT: E 189 TYR cc_start: 0.7833 (m-80) cc_final: 0.7467 (m-80) REVERT: E 268 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5742 (tp30) REVERT: E 358 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7726 (mtmm) REVERT: E 503 ASN cc_start: 0.7649 (m110) cc_final: 0.6980 (p0) outliers start: 46 outliers final: 24 residues processed: 175 average time/residue: 1.0994 time to fit residues: 213.2747 Evaluate side-chains 163 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 693 ASP Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 801 LYS Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 160 ASN D 335 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13432 Z= 0.254 Angle : 0.560 11.388 18183 Z= 0.272 Chirality : 0.041 0.325 2001 Planarity : 0.004 0.047 2267 Dihedral : 11.044 100.908 1954 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.59 % Allowed : 17.12 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.93 (0.22), residues: 1554 helix: 2.26 (0.17), residues: 929 sheet: 0.47 (0.39), residues: 179 loop : -0.46 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.002 0.001 HIS D 205 PHE 0.019 0.002 PHE E 145 TYR 0.028 0.001 TYR D 679 ARG 0.007 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 146 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: D 51 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: D 163 GLU cc_start: 0.7436 (tp30) cc_final: 0.6989 (tp30) REVERT: D 440 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: D 712 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7154 (mp) REVERT: A 44 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6597 (p) REVERT: A 85 LEU cc_start: 0.8184 (tp) cc_final: 0.7911 (tp) REVERT: A 108 ILE cc_start: 0.7738 (mt) cc_final: 0.7463 (mm) REVERT: C 122 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5906 (mmp-170) REVERT: E 112 GLU cc_start: 0.7511 (pp20) cc_final: 0.7041 (pp20) REVERT: E 177 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7394 (tpp-160) REVERT: E 189 TYR cc_start: 0.7870 (m-80) cc_final: 0.7447 (m-80) REVERT: E 268 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5755 (tp30) REVERT: E 358 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7740 (mtmm) REVERT: E 503 ASN cc_start: 0.7641 (m110) cc_final: 0.7336 (t0) REVERT: E 598 LYS cc_start: 0.4505 (OUTLIER) cc_final: 0.3965 (ptmt) outliers start: 51 outliers final: 29 residues processed: 180 average time/residue: 1.0872 time to fit residues: 217.9111 Evaluate side-chains 172 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 419 CYS Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 693 ASP Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 753 ILE Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13432 Z= 0.193 Angle : 0.542 14.595 18183 Z= 0.264 Chirality : 0.040 0.290 2001 Planarity : 0.004 0.047 2267 Dihedral : 10.724 98.841 1954 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.38 % Allowed : 17.90 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.22), residues: 1554 helix: 2.33 (0.17), residues: 929 sheet: 0.55 (0.39), residues: 179 loop : -0.45 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 268 HIS 0.002 0.000 HIS E 242 PHE 0.027 0.001 PHE B 140 TYR 0.023 0.001 TYR D 679 ARG 0.005 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: D 51 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: D 163 GLU cc_start: 0.7371 (tp30) cc_final: 0.6939 (tp30) REVERT: D 440 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: D 712 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7262 (mp) REVERT: A 44 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6585 (p) REVERT: A 85 LEU cc_start: 0.8181 (tp) cc_final: 0.7902 (tp) REVERT: B 140 PHE cc_start: 0.7662 (t80) cc_final: 0.7018 (t80) REVERT: E 112 GLU cc_start: 0.7515 (pp20) cc_final: 0.7019 (pp20) REVERT: E 189 TYR cc_start: 0.7854 (m-80) cc_final: 0.7474 (m-80) REVERT: E 268 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5749 (tp30) REVERT: E 358 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7723 (mtmm) REVERT: E 503 ASN cc_start: 0.7594 (m110) cc_final: 0.7328 (t0) REVERT: E 598 LYS cc_start: 0.4557 (OUTLIER) cc_final: 0.3973 (ptmt) REVERT: E 733 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7702 (mp0) outliers start: 48 outliers final: 23 residues processed: 176 average time/residue: 1.0887 time to fit residues: 212.5948 Evaluate side-chains 166 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 733 GLU Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 74 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 118 optimal weight: 0.0270 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13432 Z= 0.164 Angle : 0.538 14.777 18183 Z= 0.260 Chirality : 0.039 0.266 2001 Planarity : 0.004 0.047 2267 Dihedral : 10.364 96.302 1954 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.82 % Allowed : 18.60 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.22), residues: 1554 helix: 2.42 (0.17), residues: 928 sheet: 0.60 (0.39), residues: 179 loop : -0.42 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 268 HIS 0.002 0.000 HIS E 256 PHE 0.022 0.001 PHE B 140 TYR 0.020 0.001 TYR D 679 ARG 0.008 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7407 (tp30) cc_final: 0.6987 (tp30) REVERT: D 440 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: D 712 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7085 (mp) REVERT: A 44 THR cc_start: 0.6823 (OUTLIER) cc_final: 0.6611 (p) REVERT: A 85 LEU cc_start: 0.8178 (tp) cc_final: 0.7876 (tp) REVERT: E 45 LYS cc_start: 0.8228 (mttp) cc_final: 0.7792 (ptmm) REVERT: E 112 GLU cc_start: 0.7515 (pp20) cc_final: 0.6989 (pp20) REVERT: E 189 TYR cc_start: 0.7840 (m-80) cc_final: 0.7449 (m-80) REVERT: E 268 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5763 (tp30) REVERT: E 358 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7693 (mtmm) REVERT: E 533 MET cc_start: 0.1965 (tpp) cc_final: 0.1613 (tpp) REVERT: E 614 MET cc_start: 0.7770 (mpp) cc_final: 0.7317 (pp-130) REVERT: E 733 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7745 (mp0) outliers start: 40 outliers final: 22 residues processed: 168 average time/residue: 1.0881 time to fit residues: 202.4504 Evaluate side-chains 166 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 733 GLU Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 335 ASN E 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13432 Z= 0.205 Angle : 0.558 15.001 18183 Z= 0.269 Chirality : 0.040 0.266 2001 Planarity : 0.004 0.047 2267 Dihedral : 10.278 94.545 1954 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.54 % Allowed : 18.96 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.22), residues: 1554 helix: 2.39 (0.17), residues: 928 sheet: 0.68 (0.39), residues: 179 loop : -0.37 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 268 HIS 0.002 0.001 HIS D 462 PHE 0.022 0.001 PHE C 101 TYR 0.024 0.001 TYR D 679 ARG 0.013 0.000 ARG D 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7436 (tp30) cc_final: 0.7003 (tp30) REVERT: D 440 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: D 443 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7512 (mtm110) REVERT: D 712 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7126 (mp) REVERT: A 44 THR cc_start: 0.6621 (OUTLIER) cc_final: 0.6388 (p) REVERT: A 85 LEU cc_start: 0.8194 (tp) cc_final: 0.7873 (tp) REVERT: B 140 PHE cc_start: 0.7690 (t80) cc_final: 0.7080 (t80) REVERT: E 45 LYS cc_start: 0.8229 (mttp) cc_final: 0.7799 (ptmm) REVERT: E 112 GLU cc_start: 0.7614 (pp20) cc_final: 0.7019 (pp20) REVERT: E 189 TYR cc_start: 0.7831 (m-80) cc_final: 0.7449 (m-80) REVERT: E 268 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5744 (tp30) REVERT: E 358 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7702 (mtmm) REVERT: E 503 ASN cc_start: 0.6360 (t0) cc_final: 0.5777 (p0) REVERT: E 614 MET cc_start: 0.7851 (mpp) cc_final: 0.7270 (pp-130) REVERT: E 733 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7720 (mp0) outliers start: 36 outliers final: 23 residues processed: 164 average time/residue: 1.0248 time to fit residues: 187.5608 Evaluate side-chains 167 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 733 GLU Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 143 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN E 124 ASN E 402 ASN E 435 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13432 Z= 0.196 Angle : 0.562 15.120 18183 Z= 0.269 Chirality : 0.040 0.260 2001 Planarity : 0.004 0.048 2267 Dihedral : 10.137 92.612 1954 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.33 % Allowed : 19.38 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.22), residues: 1554 helix: 2.38 (0.17), residues: 928 sheet: 0.80 (0.39), residues: 177 loop : -0.37 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.002 0.001 HIS E 256 PHE 0.014 0.001 PHE D 120 TYR 0.023 0.001 TYR D 679 ARG 0.013 0.000 ARG D 443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7371 (tp30) cc_final: 0.6951 (tp30) REVERT: D 440 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: D 443 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7503 (mtm110) REVERT: D 712 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7123 (mp) REVERT: A 44 THR cc_start: 0.6689 (OUTLIER) cc_final: 0.6467 (p) REVERT: A 85 LEU cc_start: 0.8199 (tp) cc_final: 0.7873 (tp) REVERT: B 140 PHE cc_start: 0.7722 (t80) cc_final: 0.7038 (t80) REVERT: E 45 LYS cc_start: 0.8222 (mttp) cc_final: 0.7795 (ptmm) REVERT: E 112 GLU cc_start: 0.7634 (pp20) cc_final: 0.7025 (pp20) REVERT: E 189 TYR cc_start: 0.7776 (m-80) cc_final: 0.7446 (m-80) REVERT: E 268 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5744 (tp30) REVERT: E 358 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7699 (mtmm) REVERT: E 503 ASN cc_start: 0.6345 (t0) cc_final: 0.5831 (p0) REVERT: E 533 MET cc_start: 0.2159 (tpp) cc_final: 0.1835 (tpp) REVERT: E 614 MET cc_start: 0.7806 (mpp) cc_final: 0.7284 (pp-130) outliers start: 33 outliers final: 25 residues processed: 160 average time/residue: 1.0427 time to fit residues: 186.3034 Evaluate side-chains 169 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 419 CYS Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 0.0270 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 335 ASN E 124 ASN E 402 ASN E 435 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.191464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142507 restraints weight = 14816.935| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.56 r_work: 0.3604 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13432 Z= 0.186 Angle : 0.550 15.066 18183 Z= 0.265 Chirality : 0.040 0.253 2001 Planarity : 0.004 0.047 2267 Dihedral : 9.969 90.600 1954 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.75 % Allowed : 19.03 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.22), residues: 1554 helix: 2.41 (0.17), residues: 929 sheet: 0.83 (0.39), residues: 177 loop : -0.39 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.002 0.001 HIS E 256 PHE 0.029 0.001 PHE C 101 TYR 0.022 0.001 TYR D 679 ARG 0.012 0.000 ARG D 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4129.26 seconds wall clock time: 74 minutes 29.58 seconds (4469.58 seconds total)