Starting phenix.real_space_refine on Fri Mar 15 11:35:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga9_29894/03_2024/8ga9_29894.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga9_29894/03_2024/8ga9_29894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga9_29894/03_2024/8ga9_29894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga9_29894/03_2024/8ga9_29894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga9_29894/03_2024/8ga9_29894.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga9_29894/03_2024/8ga9_29894.pdb" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 S 36 5.16 5 C 3840 2.51 5 N 836 2.21 5 O 976 1.98 5 H 5864 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 125": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 368": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 449": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 576": "OE1" <-> "OE2" Residue "G ARG 615": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 623": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "G" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Time building chain proxies: 5.56, per 1000 atoms: 0.48 Number of scatterers: 11552 At special positions: 0 Unit cell: (89.385, 88.5, 61.95, 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 36 16.00 O 976 8.00 N 836 7.00 C 3840 6.00 H 5864 1.00 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: 9.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 4.236A pdb=" N LEU A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.534A pdb=" N GLN A 16 " --> pdb=" O PRO A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 40 removed outlier: 3.981A pdb=" N GLU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.509A pdb=" N LEU A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.911A pdb=" N GLU A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.511A pdb=" N PHE A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.899A pdb=" N ASN A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.679A pdb=" N LYS A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.718A pdb=" N PHE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 192 through 206 removed outlier: 4.122A pdb=" N GLU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.531A pdb=" N LEU C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 235 removed outlier: 3.786A pdb=" N GLU C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 248 removed outlier: 4.476A pdb=" N LEU C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 278 through 292 removed outlier: 3.672A pdb=" N TYR C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 289 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 305 Processing helix chain 'C' and resid 307 through 319 Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'E' and resid 334 through 342 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 358 through 372 removed outlier: 4.255A pdb=" N GLU E 364 " --> pdb=" O GLU E 360 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU E 372 " --> pdb=" O ARG E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 385 removed outlier: 3.602A pdb=" N LEU E 378 " --> pdb=" O GLY E 374 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU E 385 " --> pdb=" O ARG E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 removed outlier: 3.535A pdb=" N GLN E 391 " --> pdb=" O HIS E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 415 removed outlier: 3.572A pdb=" N PHE E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 406 " --> pdb=" O PRO E 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU E 407 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 412 " --> pdb=" O PHE E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 427 Processing helix chain 'E' and resid 430 through 443 removed outlier: 3.748A pdb=" N GLN E 434 " --> pdb=" O HIS E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 458 removed outlier: 3.683A pdb=" N LYS E 456 " --> pdb=" O PHE E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 472 removed outlier: 4.611A pdb=" N LEU E 464 " --> pdb=" O GLY E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 485 Processing helix chain 'E' and resid 487 through 497 Processing helix chain 'G' and resid 500 through 509 Processing helix chain 'G' and resid 510 through 523 removed outlier: 3.517A pdb=" N GLN G 514 " --> pdb=" O PRO G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 538 removed outlier: 4.151A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 538 " --> pdb=" O ARG G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 551 removed outlier: 3.849A pdb=" N LEU G 544 " --> pdb=" O GLY G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 566 removed outlier: 3.610A pdb=" N GLU G 566 " --> pdb=" O GLU G 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 570 through 581 removed outlier: 3.736A pdb=" N GLU G 576 " --> pdb=" O LYS G 572 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 578 " --> pdb=" O PHE G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 593 Processing helix chain 'G' and resid 596 through 609 Processing helix chain 'G' and resid 610 through 624 removed outlier: 3.670A pdb=" N LYS G 622 " --> pdb=" O PHE G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 637 Processing helix chain 'G' and resid 639 through 651 Processing helix chain 'G' and resid 653 through 662 380 hydrogen bonds defined for protein. 1140 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: 10.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 5856 1.13 - 1.31: 988 1.31 - 1.48: 2108 1.48 - 1.66: 2688 1.66 - 1.83: 64 Bond restraints: 11704 Sorted by residual: bond pdb=" CD2 PHE G 531 " pdb=" HD2 PHE G 531 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 HIS G 553 " pdb=" HE2 HIS G 553 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL E 497 " pdb=" H VAL E 497 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE1 HIS E 387 " pdb=" HE1 HIS E 387 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLN C 225 " pdb=" H GLN C 225 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 11699 not shown) Histogram of bond angle deviations from ideal: 95.95 - 102.61: 81 102.61 - 109.27: 7437 109.27 - 115.94: 7242 115.94 - 122.60: 6054 122.60 - 129.26: 598 Bond angle restraints: 21412 Sorted by residual: angle pdb=" CA ASN E 358 " pdb=" CB ASN E 358 " pdb=" CG ASN E 358 " ideal model delta sigma weight residual 112.60 118.38 -5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" C MET E 343 " pdb=" N PRO E 344 " pdb=" CA PRO E 344 " ideal model delta sigma weight residual 119.66 123.82 -4.16 7.30e-01 1.88e+00 3.25e+01 angle pdb=" CB HIS C 264 " pdb=" CG HIS C 264 " pdb=" CD2 HIS C 264 " ideal model delta sigma weight residual 131.20 124.15 7.05 1.30e+00 5.92e-01 2.94e+01 angle pdb=" CA PHE C 200 " pdb=" CB PHE C 200 " pdb=" CG PHE C 200 " ideal model delta sigma weight residual 113.80 108.44 5.36 1.00e+00 1.00e+00 2.88e+01 angle pdb=" C ASN E 401 " pdb=" N PRO E 402 " pdb=" CA PRO E 402 " ideal model delta sigma weight residual 119.82 125.06 -5.24 9.80e-01 1.04e+00 2.86e+01 ... (remaining 21407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5032 17.71 - 35.41: 283 35.41 - 53.11: 93 53.11 - 70.82: 43 70.82 - 88.52: 9 Dihedral angle restraints: 5460 sinusoidal: 2984 harmonic: 2476 Sorted by residual: dihedral pdb=" CA PHE A 77 " pdb=" C PHE A 77 " pdb=" N GLU A 78 " pdb=" CA GLU A 78 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ARG E 457 " pdb=" C ARG E 457 " pdb=" N CYS E 458 " pdb=" CA CYS E 458 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASN G 567 " pdb=" C ASN G 567 " pdb=" N PRO G 568 " pdb=" CA PRO G 568 " ideal model delta harmonic sigma weight residual 180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 527 0.087 - 0.175: 249 0.175 - 0.262: 51 0.262 - 0.349: 15 0.349 - 0.436: 2 Chirality restraints: 844 Sorted by residual: chirality pdb=" CA PHE A 77 " pdb=" N PHE A 77 " pdb=" C PHE A 77 " pdb=" CB PHE A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA PRO E 431 " pdb=" N PRO E 431 " pdb=" C PRO E 431 " pdb=" CB PRO E 431 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA MET C 167 " pdb=" N MET C 167 " pdb=" C MET C 167 " pdb=" CB MET C 167 " both_signs ideal model delta sigma weight residual False 2.57 2.24 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 841 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 155 " 0.096 2.00e-02 2.50e+03 8.84e-02 1.17e+02 pdb=" CG ASN A 155 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 155 " -0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN A 155 " -0.076 2.00e-02 2.50e+03 pdb="HD21 ASN A 155 " -0.070 2.00e-02 2.50e+03 pdb="HD22 ASN A 155 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 550 " -0.129 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG TYR G 550 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR G 550 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR G 550 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR G 550 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR G 550 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR G 550 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR G 550 " -0.118 2.00e-02 2.50e+03 pdb=" HD1 TYR G 550 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR G 550 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR G 550 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR G 550 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 25 " -0.088 2.00e-02 2.50e+03 8.19e-02 1.01e+02 pdb=" CG ASN A 25 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 25 " 0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 25 " 0.082 2.00e-02 2.50e+03 pdb="HD21 ASN A 25 " 0.060 2.00e-02 2.50e+03 pdb="HD22 ASN A 25 " -0.137 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.91: 92 1.91 - 2.59: 10184 2.59 - 3.26: 35690 3.26 - 3.93: 44115 3.93 - 4.60: 65969 Nonbonded interactions: 156050 Sorted by model distance: nonbonded pdb="HD12 LEU C 260 " pdb="HD11 LEU C 263 " model vdw 1.242 2.440 nonbonded pdb=" HE2 PHE A 116 " pdb="HD23 LEU A 161 " model vdw 1.568 2.270 nonbonded pdb="HD22 LEU A 106 " pdb="HD21 LEU A 148 " model vdw 1.614 2.440 nonbonded pdb=" O GLN A 102 " pdb="HD13 LEU A 106 " model vdw 1.636 2.620 nonbonded pdb=" OE2 GLU A 78 " pdb=" HH TYR A 122 " model vdw 1.652 1.850 ... (remaining 156045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.220 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: 0.160 Extract box with map and model: 15.400 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 41.020 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.051 5840 Z= 0.897 Angle : 1.814 8.192 7864 Z= 1.212 Chirality : 0.103 0.436 844 Planarity : 0.015 0.100 996 Dihedral : 13.583 88.525 2304 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.27), residues: 652 helix: -1.92 (0.16), residues: 584 sheet: None (None), residues: 0 loop : 1.59 (0.83), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.005 HIS G 596 PHE 0.100 0.015 PHE E 452 TYR 0.115 0.023 TYR G 550 ARG 0.015 0.003 ARG G 547 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6636 (ttpt) REVERT: C 282 PHE cc_start: 0.8393 (t80) cc_final: 0.8058 (t80) REVERT: C 312 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7999 (mppt) REVERT: E 432 MET cc_start: 0.7676 (mpp) cc_final: 0.7461 (mpp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.4097 time to fit residues: 99.3856 Evaluate side-chains 142 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN G 524 ASN G 587 GLN G 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5840 Z= 0.265 Angle : 0.775 8.696 7864 Z= 0.402 Chirality : 0.042 0.164 844 Planarity : 0.006 0.040 996 Dihedral : 5.965 28.962 708 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.90 % Allowed : 8.86 % Favored : 89.24 % 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: -1.05 (0.29), residues: 652 helix: -0.74 (0.18), residues: 597 sheet: None (None), residues: 0 loop : 2.35 (0.96), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 264 PHE 0.022 0.002 PHE E 452 TYR 0.016 0.002 TYR C 227 ARG 0.004 0.001 ARG G 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 282 PHE cc_start: 0.8314 (t80) cc_final: 0.8000 (t80) REVERT: C 312 LYS cc_start: 0.8243 (ptmt) cc_final: 0.7886 (mppt) REVERT: E 446 GLU cc_start: 0.7161 (mp0) cc_final: 0.6892 (tt0) REVERT: G 590 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8373 (mp) REVERT: G 657 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7817 (tppt) outliers start: 12 outliers final: 8 residues processed: 146 average time/residue: 0.3254 time to fit residues: 64.8507 Evaluate side-chains 138 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 630 LEU Chi-restraints excluded: chain G residue 641 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 GLN C 278 ASN E 444 ASN G 610 ASN ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5840 Z= 0.260 Angle : 0.658 8.435 7864 Z= 0.334 Chirality : 0.039 0.157 844 Planarity : 0.005 0.035 996 Dihedral : 5.432 26.093 708 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.22 % Allowed : 9.97 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.30), residues: 652 helix: -0.19 (0.19), residues: 599 sheet: None (None), residues: 0 loop : 1.52 (0.97), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 430 PHE 0.016 0.002 PHE E 452 TYR 0.011 0.002 TYR A 61 ARG 0.003 0.000 ARG G 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.6886 (m-40) cc_final: 0.6565 (m-40) REVERT: C 211 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 312 LYS cc_start: 0.8381 (ptmt) cc_final: 0.8039 (mppt) REVERT: E 424 LEU cc_start: 0.8666 (mm) cc_final: 0.8425 (mm) REVERT: E 486 GLU cc_start: 0.8175 (tt0) cc_final: 0.7941 (tp30) REVERT: G 657 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7719 (tppt) outliers start: 14 outliers final: 7 residues processed: 139 average time/residue: 0.3030 time to fit residues: 57.7911 Evaluate side-chains 131 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 630 LEU Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 GLN E 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5840 Z= 0.211 Angle : 0.600 7.479 7864 Z= 0.299 Chirality : 0.037 0.143 844 Planarity : 0.004 0.033 996 Dihedral : 5.065 25.543 708 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.06 % Allowed : 11.55 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.31), residues: 652 helix: 0.35 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 0.62 (0.98), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 387 PHE 0.012 0.001 PHE G 571 TYR 0.016 0.002 TYR C 218 ARG 0.001 0.000 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7126 (mmtt) cc_final: 0.6748 (ttpt) REVERT: A 93 ASN cc_start: 0.6830 (m-40) cc_final: 0.6527 (m-40) REVERT: C 211 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7544 (mm-30) REVERT: C 282 PHE cc_start: 0.8318 (t80) cc_final: 0.7991 (t80) REVERT: C 312 LYS cc_start: 0.8398 (ptmt) cc_final: 0.8081 (mppt) REVERT: E 424 LEU cc_start: 0.8541 (mm) cc_final: 0.8329 (mm) REVERT: E 486 GLU cc_start: 0.8158 (tt0) cc_final: 0.7779 (tp30) REVERT: G 499 MET cc_start: 0.7049 (mmp) cc_final: 0.6849 (mmt) REVERT: G 587 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6452 (tm130) REVERT: G 657 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7724 (tppt) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.3543 time to fit residues: 68.5806 Evaluate side-chains 136 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 620 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5840 Z= 0.254 Angle : 0.594 7.845 7864 Z= 0.298 Chirality : 0.037 0.160 844 Planarity : 0.004 0.036 996 Dihedral : 4.988 25.023 708 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.69 % Allowed : 12.82 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.32), residues: 652 helix: 0.49 (0.20), residues: 602 sheet: None (None), residues: 0 loop : 0.67 (1.00), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 387 PHE 0.012 0.002 PHE A 120 TYR 0.011 0.002 TYR G 550 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.6931 (m-40) cc_final: 0.6595 (m-40) REVERT: C 211 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7561 (mm-30) REVERT: C 312 LYS cc_start: 0.8437 (ptmt) cc_final: 0.8093 (mppt) REVERT: E 420 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: E 432 MET cc_start: 0.8025 (mtt) cc_final: 0.7659 (mtt) REVERT: G 586 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: G 587 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6532 (tm130) REVERT: G 657 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7759 (tppt) outliers start: 17 outliers final: 10 residues processed: 132 average time/residue: 0.3549 time to fit residues: 64.0779 Evaluate side-chains 135 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 586 GLU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 chunk 6 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5840 Z= 0.155 Angle : 0.552 5.889 7864 Z= 0.268 Chirality : 0.035 0.124 844 Planarity : 0.004 0.033 996 Dihedral : 4.610 23.871 708 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.90 % Allowed : 14.08 % Favored : 84.02 % 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: 1.23 (0.32), residues: 652 helix: 0.93 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.53 (1.04), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 387 PHE 0.013 0.001 PHE E 366 TYR 0.012 0.001 TYR A 147 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.6684 (m-40) cc_final: 0.6392 (m-40) REVERT: C 312 LYS cc_start: 0.8374 (ptmt) cc_final: 0.8048 (mppt) REVERT: G 499 MET cc_start: 0.7118 (mmp) cc_final: 0.6850 (mmt) REVERT: G 587 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6459 (tm130) REVERT: G 657 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7871 (tppt) outliers start: 12 outliers final: 7 residues processed: 136 average time/residue: 0.3349 time to fit residues: 61.8523 Evaluate side-chains 131 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5840 Z= 0.203 Angle : 0.554 6.587 7864 Z= 0.273 Chirality : 0.036 0.145 844 Planarity : 0.004 0.032 996 Dihedral : 4.571 23.397 708 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.06 % Allowed : 13.92 % Favored : 84.02 % 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: 1.22 (0.32), residues: 652 helix: 0.97 (0.20), residues: 609 sheet: None (None), residues: 0 loop : -0.20 (1.11), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 387 PHE 0.011 0.001 PHE A 120 TYR 0.012 0.001 TYR A 147 ARG 0.001 0.000 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.6759 (m-40) cc_final: 0.6438 (m-40) REVERT: C 312 LYS cc_start: 0.8445 (ptmt) cc_final: 0.8110 (mppt) REVERT: E 420 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6457 (mm-30) REVERT: E 432 MET cc_start: 0.8033 (mtt) cc_final: 0.7775 (mtt) REVERT: G 587 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6513 (tm130) outliers start: 13 outliers final: 8 residues processed: 129 average time/residue: 0.3355 time to fit residues: 58.7372 Evaluate side-chains 130 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5840 Z= 0.224 Angle : 0.560 6.921 7864 Z= 0.277 Chirality : 0.036 0.147 844 Planarity : 0.004 0.031 996 Dihedral : 4.569 23.626 708 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.06 % Allowed : 14.87 % Favored : 83.07 % 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: 1.26 (0.32), residues: 652 helix: 1.00 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.31 (1.10), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 98 PHE 0.011 0.001 PHE A 120 TYR 0.014 0.001 TYR A 147 ARG 0.002 0.001 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 312 LYS cc_start: 0.8479 (ptmt) cc_final: 0.8129 (mppt) REVERT: E 420 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6554 (mm-30) REVERT: E 432 MET cc_start: 0.8017 (mtt) cc_final: 0.7666 (mtt) REVERT: G 585 MET cc_start: 0.6678 (mmt) cc_final: 0.6427 (mmt) REVERT: G 587 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6478 (tm130) outliers start: 13 outliers final: 8 residues processed: 136 average time/residue: 0.3108 time to fit residues: 57.8505 Evaluate side-chains 135 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5840 Z= 0.187 Angle : 0.545 6.244 7864 Z= 0.268 Chirality : 0.035 0.134 844 Planarity : 0.004 0.031 996 Dihedral : 4.434 23.141 708 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.58 % Allowed : 15.35 % Favored : 83.07 % 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: 1.48 (0.33), residues: 652 helix: 1.15 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.34 (1.09), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 387 PHE 0.010 0.001 PHE E 366 TYR 0.012 0.001 TYR G 550 ARG 0.001 0.000 ARG G 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 312 LYS cc_start: 0.8469 (ptmt) cc_final: 0.8125 (mppt) REVERT: E 420 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6465 (mm-30) REVERT: E 491 LYS cc_start: 0.8577 (ttpp) cc_final: 0.7961 (tppt) REVERT: G 585 MET cc_start: 0.6628 (mmt) cc_final: 0.6361 (mmt) REVERT: G 587 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6264 (tm130) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.3380 time to fit residues: 62.8099 Evaluate side-chains 138 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5840 Z= 0.202 Angle : 0.554 6.342 7864 Z= 0.273 Chirality : 0.035 0.137 844 Planarity : 0.004 0.031 996 Dihedral : 4.414 23.542 708 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.27 % Allowed : 15.82 % Favored : 82.91 % 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: 1.49 (0.32), residues: 652 helix: 1.17 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -0.69 (1.05), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 387 PHE 0.010 0.001 PHE A 73 TYR 0.011 0.001 TYR A 79 ARG 0.002 0.000 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 312 LYS cc_start: 0.8474 (ptmt) cc_final: 0.8120 (mppt) REVERT: E 420 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6491 (mm-30) REVERT: E 491 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8213 (ttmm) REVERT: G 585 MET cc_start: 0.6638 (mmt) cc_final: 0.6373 (mmt) REVERT: G 587 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6292 (tm130) outliers start: 8 outliers final: 5 residues processed: 134 average time/residue: 0.3354 time to fit residues: 60.7720 Evaluate side-chains 138 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.174034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151641 restraints weight = 23404.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.158579 restraints weight = 11179.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162931 restraints weight = 6371.961| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5840 Z= 0.167 Angle : 0.540 5.455 7864 Z= 0.264 Chirality : 0.035 0.130 844 Planarity : 0.004 0.032 996 Dihedral : 4.289 23.209 708 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.11 % Allowed : 15.98 % Favored : 82.91 % 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: 1.86 (0.33), residues: 652 helix: 1.38 (0.21), residues: 607 sheet: None (None), residues: 0 loop : 0.01 (1.09), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 387 PHE 0.011 0.001 PHE A 73 TYR 0.013 0.001 TYR A 79 ARG 0.002 0.000 ARG G 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3427.40 seconds wall clock time: 60 minutes 37.27 seconds (3637.27 seconds total)