Starting phenix.real_space_refine on Mon Mar 11 08:49:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/03_2024/6vk3_21224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/03_2024/6vk3_21224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/03_2024/6vk3_21224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/03_2024/6vk3_21224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/03_2024/6vk3_21224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/03_2024/6vk3_21224.pdb" } resolution = 3.7 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= 0.005 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4967 2.51 5 N 1303 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4966 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 20, 'TRANS': 590} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2818 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 10, 'TRANS': 339} Chain breaks: 2 Time building chain proxies: 4.85, per 1000 atoms: 0.62 Number of scatterers: 7784 At special positions: 0 Unit cell: (103.88, 101.76, 103.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1476 8.00 N 1303 7.00 C 4967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 70 " - pdb=" SG CYS B 258 " distance=2.81 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 130 " distance=2.50 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 227 " distance=2.87 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 239 " distance=2.21 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 55.3% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 83 through 100 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.612A pdb=" N ALA A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.604A pdb=" N TYR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 314 through 331 removed outlier: 4.074A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 362 through 383 Processing helix chain 'A' and resid 390 through 407 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 429 through 442 removed outlier: 4.813A pdb=" N LYS A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.907A pdb=" N LYS A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 481 through 494 removed outlier: 3.615A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 4.190A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 4.119A pdb=" N THR A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 removed outlier: 3.539A pdb=" N LEU A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.874A pdb=" N SER A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 609 removed outlier: 4.113A pdb=" N GLY A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.750A pdb=" N ALA A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.516A pdb=" N HIS A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.714A pdb=" N ASP A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 684 Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.637A pdb=" N ILE B 49 " --> pdb=" O TRP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.785A pdb=" N MET B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 114 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.524A pdb=" N ASN B 240 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU B 242 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 243 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.688A pdb=" N TYR B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 removed outlier: 7.068A pdb=" N VAL A 61 " --> pdb=" O UNK A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 40 removed outlier: 6.193A pdb=" N LEU B 36 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS B 258 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER B 38 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 122 removed outlier: 3.962A pdb=" N VAL B 136 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 176 removed outlier: 8.895A pdb=" N TYR B 181 " --> pdb=" O CYS B 208 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS B 208 " --> pdb=" O TYR B 181 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B 229 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP B 220 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 234 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE B 218 " --> pdb=" O THR B 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 277 through 278 removed outlier: 3.528A pdb=" N ARG B 290 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 363 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN B 368 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU B 376 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 277 through 278 removed outlier: 3.528A pdb=" N ARG B 290 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 347 " --> pdb=" O LYS B 396 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1206 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: 2.14 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2453 1.34 - 1.46: 1438 1.46 - 1.58: 4006 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 7960 Sorted by residual: bond pdb=" C ARG B 116 " pdb=" N CYS B 117 " ideal model delta sigma weight residual 1.330 1.235 0.095 1.38e-02 5.25e+03 4.71e+01 bond pdb=" C CYS B 117 " pdb=" N ILE B 118 " ideal model delta sigma weight residual 1.333 1.248 0.085 1.34e-02 5.57e+03 4.04e+01 bond pdb=" CE1 HIS B 139 " pdb=" NE2 HIS B 139 " ideal model delta sigma weight residual 1.321 1.351 -0.030 1.00e-02 1.00e+04 9.25e+00 bond pdb=" N VAL B 179 " pdb=" CA VAL B 179 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.57e+00 bond pdb=" N TYR B 181 " pdb=" CA TYR B 181 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.31e-02 5.83e+03 8.52e+00 ... (remaining 7955 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.32: 200 106.32 - 113.38: 4143 113.38 - 120.44: 3403 120.44 - 127.50: 2951 127.50 - 134.56: 74 Bond angle restraints: 10771 Sorted by residual: angle pdb=" N LEU B 68 " pdb=" CA LEU B 68 " pdb=" C LEU B 68 " ideal model delta sigma weight residual 112.41 105.55 6.86 1.30e+00 5.92e-01 2.79e+01 angle pdb=" C LEU B 241 " pdb=" N GLU B 242 " pdb=" CA GLU B 242 " ideal model delta sigma weight residual 120.54 126.97 -6.43 1.35e+00 5.49e-01 2.27e+01 angle pdb=" CA ASN B 166 " pdb=" CB ASN B 166 " pdb=" CG ASN B 166 " ideal model delta sigma weight residual 112.60 117.34 -4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" C CYS B 130 " pdb=" N PRO B 131 " pdb=" CA PRO B 131 " ideal model delta sigma weight residual 119.84 125.42 -5.58 1.25e+00 6.40e-01 1.99e+01 angle pdb=" N GLU B 242 " pdb=" CA GLU B 242 " pdb=" CB GLU B 242 " ideal model delta sigma weight residual 109.94 103.38 6.56 1.49e+00 4.50e-01 1.94e+01 ... (remaining 10766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 4189 16.84 - 33.68: 446 33.68 - 50.52: 98 50.52 - 67.36: 18 67.36 - 84.21: 14 Dihedral angle restraints: 4765 sinusoidal: 1921 harmonic: 2844 Sorted by residual: dihedral pdb=" CA ASN A 516 " pdb=" C ASN A 516 " pdb=" N GLU A 517 " pdb=" CA GLU A 517 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CB CYS B 208 " pdb=" SG CYS B 208 " pdb=" SG CYS B 239 " pdb=" CB CYS B 239 " ideal model delta sinusoidal sigma weight residual -86.00 -125.09 39.09 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA ASN A 533 " pdb=" C ASN A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 949 0.065 - 0.129: 165 0.129 - 0.194: 39 0.194 - 0.259: 5 0.259 - 0.324: 2 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CB THR B 224 " pdb=" CA THR B 224 " pdb=" OG1 THR B 224 " pdb=" CG2 THR B 224 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ARG B 116 " pdb=" N ARG B 116 " pdb=" C ARG B 116 " pdb=" CB ARG B 116 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB THR B 196 " pdb=" CA THR B 196 " pdb=" OG1 THR B 196 " pdb=" CG2 THR B 196 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1157 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 125 " 0.209 2.00e-02 2.50e+03 1.05e-01 2.77e+02 pdb=" CG TRP B 125 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 125 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 125 " -0.112 2.00e-02 2.50e+03 pdb=" NE1 TRP B 125 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP B 125 " -0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP B 125 " -0.135 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 125 " 0.119 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 125 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP B 125 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 129 " 0.077 2.00e-02 2.50e+03 4.94e-02 4.88e+01 pdb=" CG TYR B 129 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR B 129 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR B 129 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR B 129 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR B 129 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR B 129 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 129 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 110 " -0.048 2.00e-02 2.50e+03 3.06e-02 1.63e+01 pdb=" CG PHE B 110 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 110 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 110 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE B 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 110 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE B 110 " -0.022 2.00e-02 2.50e+03 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 78 2.59 - 3.17: 6732 3.17 - 3.75: 11739 3.75 - 4.32: 15926 4.32 - 4.90: 26692 Nonbonded interactions: 61167 Sorted by model distance: nonbonded pdb=" O ASN B 309 " pdb=" OD1 ASN B 309 " model vdw 2.013 3.040 nonbonded pdb=" NE2 GLN B 250 " pdb=" ND2 ASN B 252 " model vdw 2.245 3.200 nonbonded pdb=" OG SER A 97 " pdb=" OG1 THR A 106 " model vdw 2.294 2.440 nonbonded pdb=" OD1 ASP A 231 " pdb=" NZ LYS A 456 " model vdw 2.305 2.520 nonbonded pdb=" CB PRO B 25 " pdb=" OH TYR B 176 " model vdw 2.307 3.440 ... (remaining 61162 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 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.660 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 24.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.006 0.095 7960 Z= 0.380 Angle : 0.934 9.296 10771 Z= 0.587 Chirality : 0.056 0.324 1160 Planarity : 0.007 0.105 1384 Dihedral : 14.845 84.206 2925 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % 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: -2.61 (0.24), residues: 940 helix: -0.92 (0.20), residues: 499 sheet: -1.96 (0.59), residues: 74 loop : -2.76 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.209 0.008 TRP B 125 HIS 0.008 0.001 HIS B 139 PHE 0.048 0.004 PHE B 110 TYR 0.086 0.002 TYR B 129 ARG 0.009 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8370 (m-30) cc_final: 0.8134 (m-30) REVERT: A 238 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8006 (mp0) REVERT: A 670 LYS cc_start: 0.6744 (mmtt) cc_final: 0.6488 (mmtt) REVERT: A 675 LYS cc_start: 0.8677 (tptm) cc_final: 0.7923 (tmmt) REVERT: B 64 MET cc_start: 0.8875 (mmt) cc_final: 0.8591 (mmt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2438 time to fit residues: 45.1223 Evaluate side-chains 98 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 123 ASN A 208 HIS A 339 ASN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 593 GLN A 611 ASN A 638 HIS B 121 GLN B 326 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7960 Z= 0.172 Angle : 0.524 6.916 10771 Z= 0.280 Chirality : 0.040 0.149 1160 Planarity : 0.003 0.042 1384 Dihedral : 4.388 21.793 1060 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.26 % Allowed : 14.39 % Favored : 83.35 % 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: -0.92 (0.27), residues: 940 helix: 0.60 (0.23), residues: 500 sheet: -1.66 (0.52), residues: 91 loop : -2.09 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 125 HIS 0.002 0.001 HIS A 638 PHE 0.014 0.001 PHE A 367 TYR 0.010 0.001 TYR A 324 ARG 0.004 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.7778 (mmm) cc_final: 0.7466 (mmm) REVERT: A 136 ASP cc_start: 0.8320 (m-30) cc_final: 0.8099 (m-30) REVERT: A 183 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7791 (mm-40) REVERT: A 347 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 639 GLU cc_start: 0.8732 (pp20) cc_final: 0.8259 (tt0) REVERT: A 670 LYS cc_start: 0.6978 (mmtt) cc_final: 0.6500 (mmtt) REVERT: A 675 LYS cc_start: 0.8567 (tptm) cc_final: 0.7845 (ttpt) REVERT: B 64 MET cc_start: 0.8913 (mmt) cc_final: 0.8712 (mmp) outliers start: 19 outliers final: 10 residues processed: 138 average time/residue: 0.1829 time to fit residues: 34.9929 Evaluate side-chains 110 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 593 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7960 Z= 0.176 Angle : 0.494 9.531 10771 Z= 0.260 Chirality : 0.039 0.136 1160 Planarity : 0.003 0.040 1384 Dihedral : 4.143 21.935 1060 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.45 % Allowed : 16.77 % Favored : 79.79 % 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 (0.27), residues: 940 helix: 1.07 (0.23), residues: 505 sheet: -1.41 (0.55), residues: 84 loop : -1.92 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 541 HIS 0.002 0.001 HIS A 143 PHE 0.010 0.001 PHE A 367 TYR 0.008 0.001 TYR A 368 ARG 0.002 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7835 (mm-40) REVERT: A 347 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8465 (mm) REVERT: A 390 ASN cc_start: 0.8796 (m-40) cc_final: 0.8514 (t0) REVERT: A 639 GLU cc_start: 0.8726 (pp20) cc_final: 0.8130 (tt0) REVERT: A 670 LYS cc_start: 0.6923 (mmtt) cc_final: 0.6413 (mmtt) REVERT: B 39 TYR cc_start: 0.8144 (m-80) cc_final: 0.7928 (m-80) REVERT: B 64 MET cc_start: 0.8950 (mmt) cc_final: 0.8708 (mmp) REVERT: B 134 GLU cc_start: 0.1630 (OUTLIER) cc_final: 0.1294 (pp20) REVERT: B 175 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5908 (mp) REVERT: B 287 TYR cc_start: 0.9100 (m-80) cc_final: 0.8807 (m-80) outliers start: 29 outliers final: 16 residues processed: 133 average time/residue: 0.1945 time to fit residues: 35.9592 Evaluate side-chains 125 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7960 Z= 0.181 Angle : 0.490 7.644 10771 Z= 0.258 Chirality : 0.039 0.144 1160 Planarity : 0.003 0.043 1384 Dihedral : 4.021 21.777 1060 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.28 % Allowed : 18.07 % Favored : 77.65 % 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: -0.07 (0.28), residues: 940 helix: 1.34 (0.23), residues: 505 sheet: -1.18 (0.58), residues: 79 loop : -1.86 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 45 HIS 0.003 0.001 HIS A 143 PHE 0.009 0.001 PHE A 452 TYR 0.009 0.001 TYR A 368 ARG 0.004 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7777 (mm-40) REVERT: A 347 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8551 (mm) REVERT: A 611 ASN cc_start: 0.7328 (t0) cc_final: 0.7125 (m-40) REVERT: A 639 GLU cc_start: 0.8743 (pp20) cc_final: 0.8232 (tt0) REVERT: A 642 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7183 (pp) REVERT: A 670 LYS cc_start: 0.6809 (mmtt) cc_final: 0.6360 (mmtt) REVERT: B 64 MET cc_start: 0.8962 (mmt) cc_final: 0.8722 (mmp) REVERT: B 175 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5980 (mp) REVERT: B 216 SER cc_start: 0.1784 (OUTLIER) cc_final: 0.0778 (t) REVERT: B 287 TYR cc_start: 0.9094 (m-80) cc_final: 0.8825 (m-80) outliers start: 36 outliers final: 19 residues processed: 139 average time/residue: 0.1741 time to fit residues: 34.0791 Evaluate side-chains 127 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7960 Z= 0.336 Angle : 0.591 9.932 10771 Z= 0.308 Chirality : 0.042 0.131 1160 Planarity : 0.003 0.042 1384 Dihedral : 4.412 23.235 1060 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.16 % Allowed : 20.10 % Favored : 75.74 % 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: -0.17 (0.27), residues: 940 helix: 1.20 (0.23), residues: 505 sheet: -1.24 (0.57), residues: 79 loop : -1.79 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 45 HIS 0.004 0.001 HIS A 143 PHE 0.010 0.001 PHE A 481 TYR 0.011 0.002 TYR B 127 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 105 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7804 (mm-40) REVERT: A 347 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 380 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8066 (m-10) REVERT: A 666 TYR cc_start: 0.8335 (t80) cc_final: 0.8070 (t80) REVERT: A 670 LYS cc_start: 0.6989 (mmtt) cc_final: 0.6532 (mptt) REVERT: B 175 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5947 (mp) REVERT: B 216 SER cc_start: 0.2725 (OUTLIER) cc_final: 0.1761 (t) REVERT: B 287 TYR cc_start: 0.9219 (m-80) cc_final: 0.8952 (m-80) outliers start: 35 outliers final: 21 residues processed: 132 average time/residue: 0.2018 time to fit residues: 37.6588 Evaluate side-chains 125 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 8.9990 chunk 18 optimal weight: 0.4980 chunk 54 optimal weight: 0.0040 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 183 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN A 593 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7960 Z= 0.161 Angle : 0.505 8.909 10771 Z= 0.261 Chirality : 0.039 0.145 1160 Planarity : 0.003 0.040 1384 Dihedral : 4.087 20.823 1060 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.92 % Allowed : 21.64 % Favored : 74.44 % 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: 0.11 (0.28), residues: 940 helix: 1.45 (0.23), residues: 504 sheet: -1.08 (0.58), residues: 79 loop : -1.71 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 45 HIS 0.003 0.001 HIS A 122 PHE 0.008 0.001 PHE A 201 TYR 0.011 0.001 TYR A 368 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.8814 (ttm) cc_final: 0.8481 (mtp) REVERT: A 183 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7641 (mm-40) REVERT: A 347 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8374 (mm) REVERT: A 380 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8013 (m-10) REVERT: A 611 ASN cc_start: 0.7483 (t0) cc_final: 0.7159 (m-40) REVERT: A 670 LYS cc_start: 0.6947 (mmtt) cc_final: 0.6505 (mmtt) REVERT: B 216 SER cc_start: 0.2730 (OUTLIER) cc_final: 0.1785 (t) REVERT: B 287 TYR cc_start: 0.9157 (m-80) cc_final: 0.8897 (m-80) outliers start: 33 outliers final: 22 residues processed: 134 average time/residue: 0.1697 time to fit residues: 32.3581 Evaluate side-chains 131 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7960 Z= 0.171 Angle : 0.513 8.296 10771 Z= 0.264 Chirality : 0.039 0.170 1160 Planarity : 0.003 0.049 1384 Dihedral : 3.997 21.199 1060 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.92 % Allowed : 22.71 % Favored : 73.37 % 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: 0.22 (0.28), residues: 940 helix: 1.54 (0.23), residues: 505 sheet: -0.96 (0.59), residues: 79 loop : -1.67 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 45 HIS 0.003 0.001 HIS A 122 PHE 0.008 0.001 PHE A 452 TYR 0.010 0.001 TYR A 368 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7880 (mmm) cc_final: 0.7576 (mmm) REVERT: A 152 MET cc_start: 0.8816 (ttm) cc_final: 0.8538 (mtp) REVERT: A 183 GLN cc_start: 0.8166 (mt0) cc_final: 0.7880 (mm-40) REVERT: A 347 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 380 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8030 (m-10) REVERT: A 611 ASN cc_start: 0.7494 (t0) cc_final: 0.7164 (m-40) REVERT: B 216 SER cc_start: 0.2781 (OUTLIER) cc_final: 0.1838 (t) REVERT: B 287 TYR cc_start: 0.9132 (m-80) cc_final: 0.8891 (m-80) outliers start: 33 outliers final: 21 residues processed: 137 average time/residue: 0.1631 time to fit residues: 31.9960 Evaluate side-chains 129 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.0030 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 0.0030 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN B 139 HIS B 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7960 Z= 0.140 Angle : 0.502 7.978 10771 Z= 0.257 Chirality : 0.038 0.146 1160 Planarity : 0.003 0.044 1384 Dihedral : 3.882 20.698 1060 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.57 % Allowed : 22.47 % Favored : 73.96 % 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: 0.34 (0.28), residues: 940 helix: 1.64 (0.24), residues: 504 sheet: -0.87 (0.59), residues: 79 loop : -1.64 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 45 HIS 0.002 0.001 HIS A 122 PHE 0.008 0.001 PHE A 201 TYR 0.009 0.001 TYR A 368 ARG 0.002 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7834 (mmm) cc_final: 0.7538 (mmm) REVERT: A 152 MET cc_start: 0.8789 (ttm) cc_final: 0.8482 (mtp) REVERT: A 183 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7619 (mm-40) REVERT: A 334 TYR cc_start: 0.8683 (m-10) cc_final: 0.8405 (m-80) REVERT: A 380 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: A 428 ASN cc_start: 0.7535 (m-40) cc_final: 0.6686 (t0) REVERT: A 444 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7727 (tp40) REVERT: A 478 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9247 (mm) REVERT: A 611 ASN cc_start: 0.7421 (t0) cc_final: 0.7137 (m-40) REVERT: B 51 GLN cc_start: 0.6691 (mm110) cc_final: 0.6463 (mm-40) REVERT: B 216 SER cc_start: 0.2620 (OUTLIER) cc_final: 0.1665 (t) REVERT: B 287 TYR cc_start: 0.9095 (m-80) cc_final: 0.8855 (m-80) outliers start: 30 outliers final: 19 residues processed: 143 average time/residue: 0.1637 time to fit residues: 33.8836 Evaluate side-chains 132 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 371 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 661 HIS B 73 GLN B 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7960 Z= 0.170 Angle : 0.527 9.211 10771 Z= 0.268 Chirality : 0.039 0.148 1160 Planarity : 0.003 0.044 1384 Dihedral : 3.900 21.124 1060 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.80 % Allowed : 22.35 % Favored : 73.84 % 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: 0.33 (0.28), residues: 940 helix: 1.59 (0.24), residues: 504 sheet: -0.83 (0.57), residues: 79 loop : -1.59 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 45 HIS 0.002 0.001 HIS A 122 PHE 0.009 0.001 PHE B 71 TYR 0.010 0.001 TYR A 74 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7873 (mmm) cc_final: 0.7567 (mmm) REVERT: A 152 MET cc_start: 0.8820 (ttm) cc_final: 0.8517 (mtp) REVERT: A 183 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7626 (mm-40) REVERT: A 334 TYR cc_start: 0.8708 (m-10) cc_final: 0.8476 (m-80) REVERT: A 380 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7951 (m-10) REVERT: A 428 ASN cc_start: 0.7543 (m-40) cc_final: 0.6653 (t0) REVERT: A 444 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7764 (tp40) REVERT: A 478 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9250 (mm) REVERT: A 611 ASN cc_start: 0.7503 (t0) cc_final: 0.7162 (m-40) REVERT: B 51 GLN cc_start: 0.6639 (mm110) cc_final: 0.6420 (mm-40) REVERT: B 216 SER cc_start: 0.2688 (OUTLIER) cc_final: 0.1725 (t) outliers start: 32 outliers final: 22 residues processed: 133 average time/residue: 0.1686 time to fit residues: 32.5501 Evaluate side-chains 131 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 371 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 374 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN B 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7960 Z= 0.171 Angle : 0.532 9.112 10771 Z= 0.269 Chirality : 0.039 0.146 1160 Planarity : 0.003 0.043 1384 Dihedral : 3.888 21.162 1060 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.45 % Allowed : 22.71 % Favored : 73.84 % 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: 0.36 (0.28), residues: 940 helix: 1.60 (0.24), residues: 504 sheet: -0.81 (0.57), residues: 79 loop : -1.55 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 45 HIS 0.002 0.000 HIS A 122 PHE 0.008 0.001 PHE B 71 TYR 0.010 0.001 TYR A 563 ARG 0.003 0.000 ARG B 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7873 (mmm) cc_final: 0.7565 (mmm) REVERT: A 152 MET cc_start: 0.8826 (ttm) cc_final: 0.8495 (mtp) REVERT: A 183 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7735 (mm-40) REVERT: A 334 TYR cc_start: 0.8714 (m-10) cc_final: 0.8477 (m-80) REVERT: A 380 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: A 428 ASN cc_start: 0.7609 (m-40) cc_final: 0.6746 (t0) REVERT: A 444 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7756 (tp40) REVERT: A 478 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9256 (mm) REVERT: A 611 ASN cc_start: 0.7460 (t0) cc_final: 0.7098 (m-40) REVERT: A 639 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: B 51 GLN cc_start: 0.6596 (mm110) cc_final: 0.6376 (mm-40) REVERT: B 216 SER cc_start: 0.2758 (OUTLIER) cc_final: 0.1789 (t) REVERT: B 319 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7873 (tm-30) outliers start: 29 outliers final: 22 residues processed: 129 average time/residue: 0.1707 time to fit residues: 32.1641 Evaluate side-chains 133 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 371 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 0.0050 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN B 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.203112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153406 restraints weight = 9859.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.153088 restraints weight = 9753.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154415 restraints weight = 9481.045| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7960 Z= 0.172 Angle : 0.532 8.870 10771 Z= 0.269 Chirality : 0.039 0.162 1160 Planarity : 0.003 0.043 1384 Dihedral : 3.910 21.125 1060 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.45 % Allowed : 22.83 % Favored : 73.72 % 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: 0.35 (0.27), residues: 940 helix: 1.61 (0.24), residues: 503 sheet: -0.83 (0.57), residues: 79 loop : -1.55 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 45 HIS 0.002 0.000 HIS A 122 PHE 0.008 0.001 PHE B 71 TYR 0.008 0.001 TYR A 368 ARG 0.003 0.000 ARG B 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.68 seconds wall clock time: 31 minutes 57.46 seconds (1917.46 seconds total)