Starting phenix.real_space_refine on Sun Mar 10 23:40:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/03_2024/7n0c_24103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/03_2024/7n0c_24103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/03_2024/7n0c_24103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/03_2024/7n0c_24103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/03_2024/7n0c_24103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0c_24103/03_2024/7n0c_24103.pdb" } resolution = 3.4 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= 0.079 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 49 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 3685 2.51 5 N 1033 2.21 5 O 1262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 64": "OD1" <-> "OD2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B ASP 10": "OD1" <-> "OD2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B ASP 273": "OD1" <-> "OD2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 402": "OD1" <-> "OD2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 496": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6088 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4090 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 26, 'TRANS': 486} Chain breaks: 1 Chain: "T" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 23} Chain: "D" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 506 Classifications: {'RNA': 24} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 2, ' ZN': 3} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 40.023 24.791 92.919 1.00 51.61 S ATOM 546 SG CYS A 77 36.858 25.756 93.856 1.00 51.71 S ATOM 651 SG CYS A 90 37.756 22.498 94.187 1.00 57.18 S ATOM 854 SG CYS A 117 52.155 10.429 99.974 1.00112.87 S ATOM 874 SG CYS A 120 52.595 10.897 103.370 1.00118.76 S ATOM 935 SG CYS A 128 55.207 11.780 101.062 1.00109.13 S ATOM 947 SG CYS A 130 55.533 8.590 102.165 1.00128.22 S ATOM 2582 SG CYS B 207 44.467 25.564 61.321 1.00 62.28 S ATOM 2602 SG CYS B 210 45.850 26.017 57.879 1.00 73.07 S ATOM 2723 SG CYS B 226 43.066 27.801 59.072 1.00 56.89 S ATOM 3023 SG CYS B 261 24.861 55.828 57.812 1.00 65.13 S ATOM 3153 SG CYS B 279 27.911 54.398 59.550 1.00 44.17 S ATOM 4543 SG CYS B 452 49.557 45.528 11.477 1.00134.04 S ATOM 4657 SG CYS B 477 45.734 45.992 12.975 1.00138.24 S ATOM 4699 SG CYS B 484 48.139 43.581 13.594 1.00139.40 S Time building chain proxies: 4.03, per 1000 atoms: 0.66 Number of scatterers: 6088 At special positions: 0 Unit cell: (70.488, 89.712, 144.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 52 16.00 P 49 15.00 Mg 2 11.99 O 1262 8.00 N 1033 7.00 C 3685 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: 2.62 Conformation dependent library (CDL) restraints added in 975.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 207 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 279 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 261 " pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 477 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 452 " Number of angles added : 17 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1204 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 26.6% alpha, 12.1% beta 23 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 4.249A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.067A pdb=" N LYS A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.595A pdb=" N VAL B 29 " --> pdb=" O HIS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.844A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.850A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.654A pdb=" N ASP B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.841A pdb=" N CYS B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 removed outlier: 3.584A pdb=" N ASN B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.931A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.589A pdb=" N GLY B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 505 removed outlier: 4.313A pdb=" N ASN B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.754A pdb=" N ASN B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.365A pdb=" N TYR B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118 removed outlier: 5.519A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 225 removed outlier: 3.726A pdb=" N THR B 223 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.020A pdb=" N LEU B 329 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR B 351 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP B 331 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 381 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 401 Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 447 removed outlier: 5.938A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 125 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 860 1.29 - 1.42: 2016 1.42 - 1.56: 3298 1.56 - 1.69: 97 1.69 - 1.83: 68 Bond restraints: 6339 Sorted by residual: bond pdb=" C PRO B 106 " pdb=" O PRO B 106 " ideal model delta sigma weight residual 1.233 1.151 0.082 1.06e-02 8.90e+03 6.06e+01 bond pdb=" CA PRO B 106 " pdb=" CB PRO B 106 " ideal model delta sigma weight residual 1.533 1.485 0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" N LEU B 105 " pdb=" CA LEU B 105 " ideal model delta sigma weight residual 1.452 1.499 -0.047 1.41e-02 5.03e+03 1.12e+01 bond pdb=" C ASN B 104 " pdb=" O ASN B 104 " ideal model delta sigma weight residual 1.234 1.195 0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" C LEU B 105 " pdb=" N PRO B 106 " ideal model delta sigma weight residual 1.334 1.368 -0.034 1.11e-02 8.12e+03 9.49e+00 ... (remaining 6334 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.00: 329 105.00 - 112.31: 3228 112.31 - 119.62: 2109 119.62 - 126.93: 2979 126.93 - 134.24: 196 Bond angle restraints: 8841 Sorted by residual: angle pdb=" CA PRO B 106 " pdb=" C PRO B 106 " pdb=" O PRO B 106 " ideal model delta sigma weight residual 120.97 111.88 9.09 1.17e+00 7.31e-01 6.03e+01 angle pdb=" C PRO B 106 " pdb=" CA PRO B 106 " pdb=" CB PRO B 106 " ideal model delta sigma weight residual 111.11 103.39 7.72 1.17e+00 7.31e-01 4.35e+01 angle pdb=" CA PRO B 106 " pdb=" C PRO B 106 " pdb=" N LEU B 107 " ideal model delta sigma weight residual 115.93 123.67 -7.74 1.26e+00 6.30e-01 3.78e+01 angle pdb=" CA LEU B 105 " pdb=" C LEU B 105 " pdb=" N PRO B 106 " ideal model delta sigma weight residual 117.67 123.60 -5.93 1.01e+00 9.80e-01 3.45e+01 angle pdb=" N VAL B 167 " pdb=" CA VAL B 167 " pdb=" C VAL B 167 " ideal model delta sigma weight residual 112.90 107.43 5.47 9.60e-01 1.09e+00 3.24e+01 ... (remaining 8836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 3624 34.34 - 68.68: 129 68.68 - 103.02: 12 103.02 - 137.36: 0 137.36 - 171.70: 1 Dihedral angle restraints: 3766 sinusoidal: 1891 harmonic: 1875 Sorted by residual: dihedral pdb=" O4' U T 6 " pdb=" C1' U T 6 " pdb=" N1 U T 6 " pdb=" C2 U T 6 " ideal model delta sinusoidal sigma weight residual 232.00 60.30 171.70 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" CA HIS B 268 " pdb=" C HIS B 268 " pdb=" N VAL B 269 " pdb=" CA VAL B 269 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA TYR B 237 " pdb=" C TYR B 237 " pdb=" N ASN B 238 " pdb=" CA ASN B 238 " ideal model delta harmonic sigma weight residual -180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 671 0.041 - 0.083: 237 0.083 - 0.124: 74 0.124 - 0.166: 21 0.166 - 0.207: 12 Chirality restraints: 1015 Sorted by residual: chirality pdb=" CA ASN B 478 " pdb=" N ASN B 478 " pdb=" C ASN B 478 " pdb=" CB ASN B 478 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA CYS B 210 " pdb=" N CYS B 210 " pdb=" C CYS B 210 " pdb=" CB CYS B 210 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ASP B 415 " pdb=" N ASP B 415 " pdb=" C ASP B 415 " pdb=" CB ASP B 415 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1012 not shown) Planarity restraints: 953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 487 " -0.060 2.00e-02 2.50e+03 4.49e-02 3.02e+01 pdb=" CG HIS B 487 " 0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS B 487 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS B 487 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 HIS B 487 " -0.039 2.00e-02 2.50e+03 pdb=" NE2 HIS B 487 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 229 " -0.053 2.00e-02 2.50e+03 4.01e-02 2.41e+01 pdb=" CG HIS B 229 " 0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS B 229 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS B 229 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS B 229 " -0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS B 229 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 83 " 0.044 2.00e-02 2.50e+03 3.24e-02 1.58e+01 pdb=" CG HIS A 83 " -0.047 2.00e-02 2.50e+03 pdb=" ND1 HIS A 83 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 83 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A 83 " 0.028 2.00e-02 2.50e+03 pdb=" NE2 HIS A 83 " 0.019 2.00e-02 2.50e+03 ... (remaining 950 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 510 2.72 - 3.27: 5827 3.27 - 3.81: 10466 3.81 - 4.36: 12799 4.36 - 4.90: 20376 Nonbonded interactions: 49978 Sorted by model distance: nonbonded pdb=" OD1 ASP B 90 " pdb="MG MG B 602 " model vdw 2.180 2.170 nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.216 2.170 nonbonded pdb=" O ILE B 80 " pdb=" OH TYR B 296 " model vdw 2.221 2.440 nonbonded pdb=" OG SER B 171 " pdb=" O TRP B 227 " model vdw 2.226 2.440 nonbonded pdb=" OE1 GLU B 302 " pdb=" ND2 ASN B 422 " model vdw 2.257 2.520 ... (remaining 49973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.780 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.370 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.009 0.082 6339 Z= 0.571 Angle : 0.996 9.085 8841 Z= 0.611 Chirality : 0.052 0.207 1015 Planarity : 0.007 0.059 953 Dihedral : 16.673 171.703 2562 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % 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: -3.80 (0.27), residues: 638 helix: -3.43 (0.29), residues: 142 sheet: -2.66 (0.62), residues: 49 loop : -2.34 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 385 HIS 0.011 0.003 HIS B 257 PHE 0.040 0.003 PHE A 19 TYR 0.022 0.002 TYR A 76 ARG 0.005 0.001 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7961 (mmtp) REVERT: A 98 GLN cc_start: 0.8060 (mp-120) cc_final: 0.7752 (mm110) REVERT: A 114 ASN cc_start: 0.8736 (m-40) cc_final: 0.8522 (m110) REVERT: B 58 MET cc_start: 0.8765 (mtp) cc_final: 0.8335 (mtp) REVERT: B 169 MET cc_start: 0.8659 (ttp) cc_final: 0.7961 (tmm) REVERT: B 330 HIS cc_start: 0.7916 (m-70) cc_final: 0.6908 (m-70) REVERT: B 499 ASN cc_start: 0.7843 (m-40) cc_final: 0.7558 (m-40) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2181 time to fit residues: 29.4448 Evaluate side-chains 88 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN B 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6339 Z= 0.225 Angle : 0.537 5.608 8841 Z= 0.281 Chirality : 0.040 0.150 1015 Planarity : 0.005 0.055 953 Dihedral : 16.286 172.600 1417 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.99 % Allowed : 11.75 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.29), residues: 638 helix: -2.07 (0.39), residues: 142 sheet: -2.72 (0.60), residues: 48 loop : -1.94 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 385 HIS 0.005 0.001 HIS B 257 PHE 0.014 0.001 PHE B 133 TYR 0.024 0.001 TYR B 370 ARG 0.004 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8431 (t) cc_final: 0.8216 (t) REVERT: B 58 MET cc_start: 0.8743 (mtp) cc_final: 0.8232 (mtp) REVERT: B 61 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8621 (mtpp) REVERT: B 169 MET cc_start: 0.8564 (ttp) cc_final: 0.8166 (tmm) REVERT: B 330 HIS cc_start: 0.7393 (m-70) cc_final: 0.6493 (m170) REVERT: B 391 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7633 (mtp180) REVERT: B 395 ASN cc_start: 0.8311 (p0) cc_final: 0.8045 (p0) REVERT: B 499 ASN cc_start: 0.7665 (m110) cc_final: 0.7447 (m110) outliers start: 11 outliers final: 6 residues processed: 106 average time/residue: 0.1771 time to fit residues: 24.9282 Evaluate side-chains 91 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 223 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 0.0020 chunk 17 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6339 Z= 0.171 Angle : 0.498 5.692 8841 Z= 0.255 Chirality : 0.039 0.139 1015 Planarity : 0.004 0.075 953 Dihedral : 16.092 172.848 1417 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.89 % Allowed : 12.30 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.31), residues: 638 helix: -1.54 (0.41), residues: 149 sheet: -2.33 (0.56), residues: 62 loop : -1.54 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 520 HIS 0.003 0.001 HIS B 257 PHE 0.013 0.001 PHE B 384 TYR 0.017 0.001 TYR B 446 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8348 (t) cc_final: 0.8097 (t) REVERT: A 114 ASN cc_start: 0.8657 (m-40) cc_final: 0.8445 (m110) REVERT: B 58 MET cc_start: 0.8739 (mtp) cc_final: 0.8228 (mtp) REVERT: B 61 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8540 (mtpp) REVERT: B 169 MET cc_start: 0.8527 (ttp) cc_final: 0.8311 (ptm) REVERT: B 330 HIS cc_start: 0.7451 (m-70) cc_final: 0.6926 (m170) REVERT: B 352 ASP cc_start: 0.6407 (t0) cc_final: 0.6111 (t70) REVERT: B 391 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7669 (mtp180) REVERT: B 395 ASN cc_start: 0.8386 (p0) cc_final: 0.8009 (p0) REVERT: B 398 VAL cc_start: 0.8963 (t) cc_final: 0.8605 (p) outliers start: 16 outliers final: 12 residues processed: 107 average time/residue: 0.1693 time to fit residues: 24.3920 Evaluate side-chains 103 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6339 Z= 0.207 Angle : 0.495 6.026 8841 Z= 0.253 Chirality : 0.039 0.142 1015 Planarity : 0.004 0.056 953 Dihedral : 15.997 172.912 1417 Min Nonbonded Distance : 1.244 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.07 % Allowed : 13.20 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.31), residues: 638 helix: -1.12 (0.44), residues: 143 sheet: -2.58 (0.53), residues: 68 loop : -1.32 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 520 HIS 0.003 0.001 HIS B 257 PHE 0.016 0.001 PHE B 350 TYR 0.018 0.001 TYR B 447 ARG 0.002 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8272 (t) cc_final: 0.8030 (t) REVERT: B 58 MET cc_start: 0.8750 (mtp) cc_final: 0.8241 (mtp) REVERT: B 61 LYS cc_start: 0.8848 (mtpt) cc_final: 0.8512 (mtpp) REVERT: B 169 MET cc_start: 0.8578 (ttp) cc_final: 0.8311 (ptm) REVERT: B 185 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 330 HIS cc_start: 0.7514 (m-70) cc_final: 0.6839 (m170) REVERT: B 391 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7735 (mtp180) REVERT: B 395 ASN cc_start: 0.8438 (p0) cc_final: 0.8127 (p0) REVERT: B 398 VAL cc_start: 0.8983 (t) cc_final: 0.8614 (p) REVERT: B 445 PHE cc_start: 0.8917 (p90) cc_final: 0.8684 (p90) outliers start: 17 outliers final: 14 residues processed: 106 average time/residue: 0.1664 time to fit residues: 23.7418 Evaluate side-chains 108 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 382 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 0.0470 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 2.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 6339 Z= 0.565 Angle : 0.653 5.476 8841 Z= 0.341 Chirality : 0.045 0.164 1015 Planarity : 0.005 0.036 953 Dihedral : 16.195 171.371 1417 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.52 % Allowed : 13.74 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.31), residues: 638 helix: -1.53 (0.41), residues: 148 sheet: -2.68 (0.54), residues: 62 loop : -1.58 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 227 HIS 0.005 0.001 HIS A 83 PHE 0.032 0.003 PHE A 19 TYR 0.025 0.002 TYR B 51 ARG 0.008 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8401 (t) cc_final: 0.8195 (t) REVERT: B 58 MET cc_start: 0.8861 (mtp) cc_final: 0.8283 (mtp) REVERT: B 61 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8562 (mtpp) REVERT: B 169 MET cc_start: 0.8692 (ttp) cc_final: 0.8326 (tmm) REVERT: B 185 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 330 HIS cc_start: 0.7268 (m-70) cc_final: 0.6649 (m170) REVERT: B 395 ASN cc_start: 0.8447 (p0) cc_final: 0.8074 (p0) REVERT: B 398 VAL cc_start: 0.9050 (t) cc_final: 0.8668 (p) outliers start: 25 outliers final: 21 residues processed: 103 average time/residue: 0.1617 time to fit residues: 22.6899 Evaluate side-chains 105 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6339 Z= 0.191 Angle : 0.499 6.850 8841 Z= 0.257 Chirality : 0.039 0.177 1015 Planarity : 0.004 0.031 953 Dihedral : 16.077 172.233 1417 Min Nonbonded Distance : 1.095 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.98 % Allowed : 15.55 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.32), residues: 638 helix: -1.10 (0.44), residues: 143 sheet: -2.56 (0.55), residues: 54 loop : -1.31 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 PHE 0.019 0.001 PHE B 350 TYR 0.019 0.001 TYR B 370 ARG 0.006 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8151 (t) cc_final: 0.7889 (t) REVERT: B 58 MET cc_start: 0.8775 (mtp) cc_final: 0.8494 (mtp) REVERT: B 61 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8573 (mtpp) REVERT: B 71 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7923 (t0) REVERT: B 169 MET cc_start: 0.8516 (ttp) cc_final: 0.8261 (ptm) REVERT: B 185 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8234 (mt) REVERT: B 330 HIS cc_start: 0.7186 (m-70) cc_final: 0.6708 (m170) REVERT: B 370 TYR cc_start: 0.8102 (t80) cc_final: 0.7742 (t80) REVERT: B 391 ARG cc_start: 0.8321 (mtp180) cc_final: 0.7597 (mtp180) REVERT: B 395 ASN cc_start: 0.8517 (p0) cc_final: 0.8250 (p0) outliers start: 22 outliers final: 16 residues processed: 105 average time/residue: 0.1609 time to fit residues: 22.9123 Evaluate side-chains 110 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 382 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6339 Z= 0.218 Angle : 0.504 5.808 8841 Z= 0.258 Chirality : 0.039 0.174 1015 Planarity : 0.003 0.031 953 Dihedral : 15.988 172.341 1417 Min Nonbonded Distance : 1.103 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.80 % Allowed : 16.82 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.33), residues: 638 helix: -0.98 (0.44), residues: 143 sheet: -2.67 (0.51), residues: 74 loop : -1.10 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 PHE 0.013 0.001 PHE A 19 TYR 0.014 0.001 TYR B 446 ARG 0.005 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8174 (t) cc_final: 0.7934 (t) REVERT: A 98 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7392 (mm-40) REVERT: B 58 MET cc_start: 0.8787 (mtp) cc_final: 0.8509 (mtp) REVERT: B 61 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8513 (mtpp) REVERT: B 169 MET cc_start: 0.8548 (ttp) cc_final: 0.8234 (ptm) REVERT: B 315 MET cc_start: 0.8436 (tmm) cc_final: 0.8216 (tmm) REVERT: B 330 HIS cc_start: 0.7381 (m-70) cc_final: 0.6564 (m170) REVERT: B 370 TYR cc_start: 0.8087 (t80) cc_final: 0.7853 (t80) REVERT: B 395 ASN cc_start: 0.8574 (p0) cc_final: 0.8303 (p0) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.1515 time to fit residues: 22.5679 Evaluate side-chains 110 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 382 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6339 Z= 0.202 Angle : 0.493 6.719 8841 Z= 0.253 Chirality : 0.039 0.180 1015 Planarity : 0.003 0.030 953 Dihedral : 15.941 172.454 1417 Min Nonbonded Distance : 1.104 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.62 % Allowed : 17.54 % Favored : 78.84 % 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: -1.81 (0.32), residues: 638 helix: -0.88 (0.44), residues: 143 sheet: -2.31 (0.57), residues: 54 loop : -1.20 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 PHE 0.019 0.001 PHE B 350 TYR 0.015 0.001 TYR B 446 ARG 0.004 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8150 (t) cc_final: 0.7906 (t) REVERT: B 58 MET cc_start: 0.8775 (mtp) cc_final: 0.8492 (mtp) REVERT: B 61 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8531 (mtpp) REVERT: B 169 MET cc_start: 0.8559 (ttp) cc_final: 0.8253 (ptm) REVERT: B 195 MET cc_start: 0.8651 (mtp) cc_final: 0.8409 (mtm) REVERT: B 330 HIS cc_start: 0.7265 (m-70) cc_final: 0.6778 (m-70) REVERT: B 395 ASN cc_start: 0.8557 (p0) cc_final: 0.8283 (p0) REVERT: B 398 VAL cc_start: 0.8878 (t) cc_final: 0.8550 (p) outliers start: 20 outliers final: 18 residues processed: 100 average time/residue: 0.1624 time to fit residues: 22.1351 Evaluate side-chains 111 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 382 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 57 optimal weight: 0.0980 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6339 Z= 0.194 Angle : 0.515 10.551 8841 Z= 0.256 Chirality : 0.039 0.178 1015 Planarity : 0.003 0.028 953 Dihedral : 15.882 172.589 1417 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.44 % Allowed : 17.36 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.33), residues: 638 helix: -0.70 (0.44), residues: 143 sheet: -2.43 (0.52), residues: 74 loop : -0.94 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 PHE 0.015 0.001 PHE B 350 TYR 0.017 0.001 TYR B 446 ARG 0.005 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8118 (t) cc_final: 0.7880 (t) REVERT: A 98 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7286 (mm-40) REVERT: B 58 MET cc_start: 0.8770 (mtp) cc_final: 0.8484 (mtp) REVERT: B 61 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8524 (mtpp) REVERT: B 169 MET cc_start: 0.8570 (ttp) cc_final: 0.8252 (ptm) REVERT: B 330 HIS cc_start: 0.7423 (m-70) cc_final: 0.6796 (m-70) REVERT: B 395 ASN cc_start: 0.8538 (p0) cc_final: 0.8322 (p0) REVERT: B 398 VAL cc_start: 0.8894 (t) cc_final: 0.8586 (p) REVERT: B 445 PHE cc_start: 0.8833 (p90) cc_final: 0.8508 (p90) outliers start: 19 outliers final: 18 residues processed: 101 average time/residue: 0.1578 time to fit residues: 21.9886 Evaluate side-chains 109 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 382 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 0.0070 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6339 Z= 0.151 Angle : 0.500 11.958 8841 Z= 0.248 Chirality : 0.038 0.192 1015 Planarity : 0.003 0.026 953 Dihedral : 15.777 172.981 1417 Min Nonbonded Distance : 1.163 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.07 % Allowed : 17.36 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.33), residues: 638 helix: -0.71 (0.43), residues: 143 sheet: -1.95 (0.62), residues: 48 loop : -0.90 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 520 HIS 0.006 0.001 HIS B 487 PHE 0.018 0.001 PHE B 444 TYR 0.027 0.001 TYR B 447 ARG 0.005 0.000 ARG A 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8050 (t) cc_final: 0.7795 (t) REVERT: B 58 MET cc_start: 0.8724 (mtp) cc_final: 0.8418 (mtp) REVERT: B 61 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8461 (mtpp) REVERT: B 169 MET cc_start: 0.8532 (ttp) cc_final: 0.8243 (ptm) REVERT: B 195 MET cc_start: 0.8606 (mtp) cc_final: 0.8335 (mtm) REVERT: B 330 HIS cc_start: 0.7231 (m-70) cc_final: 0.6868 (m-70) REVERT: B 398 VAL cc_start: 0.8771 (t) cc_final: 0.8504 (p) REVERT: B 445 PHE cc_start: 0.8769 (p90) cc_final: 0.8419 (p90) outliers start: 17 outliers final: 15 residues processed: 102 average time/residue: 0.1602 time to fit residues: 22.1387 Evaluate side-chains 109 residues out of total 553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 0.0050 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.0270 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.0020 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.2460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN B 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.182243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126121 restraints weight = 7343.503| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.11 r_work: 0.3111 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6339 Z= 0.149 Angle : 0.510 13.543 8841 Z= 0.254 Chirality : 0.038 0.182 1015 Planarity : 0.003 0.036 953 Dihedral : 15.654 173.441 1417 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.07 % Allowed : 17.36 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.33), residues: 638 helix: -0.77 (0.42), residues: 149 sheet: -2.13 (0.57), residues: 66 loop : -0.62 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 520 HIS 0.002 0.001 HIS B 283 PHE 0.015 0.001 PHE B 350 TYR 0.017 0.001 TYR B 446 ARG 0.004 0.000 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1620.81 seconds wall clock time: 30 minutes 9.66 seconds (1809.66 seconds total)