Starting phenix.real_space_refine on Sun Mar 10 23:01:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/03_2024/8gni_34165_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/03_2024/8gni_34165.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/03_2024/8gni_34165_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/03_2024/8gni_34165_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/03_2024/8gni_34165_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/03_2024/8gni_34165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/03_2024/8gni_34165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/03_2024/8gni_34165_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/03_2024/8gni_34165_updated.pdb" } resolution = 3.74 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 28 5.16 5 C 3670 2.51 5 N 1042 2.21 5 O 1091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" 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: 5832 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3821 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain: "B" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1125 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "C" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.64, per 1000 atoms: 0.62 Number of scatterers: 5832 At special positions: 0 Unit cell: (86.08, 100.068, 119.436, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 1 15.00 O 1091 8.00 N 1042 7.00 C 3670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 96 " distance=2.04 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 3 sheets defined 49.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 59 through 80 removed outlier: 3.695A pdb=" N ASP A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.648A pdb=" N GLY A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 111 through 121 removed outlier: 4.849A pdb=" N ASP A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 139 through 142 No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.744A pdb=" N GLU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.976A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 178 through 192 removed outlier: 3.809A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.993A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.720A pdb=" N GLY A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 255 through 258 No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 281 through 290 removed outlier: 4.304A pdb=" N ARG A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.518A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 327 through 334 Proline residue: A 332 - end of helix Processing helix chain 'A' and resid 339 through 358 removed outlier: 4.176A pdb=" N LEU A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.548A pdb=" N VAL A 364 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 removed outlier: 3.625A pdb=" N LEU A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 427 through 435 removed outlier: 4.877A pdb=" N GLU A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.956A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 508 removed outlier: 4.398A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 505 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'B' and resid 575 through 586 Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 638 through 649 removed outlier: 4.245A pdb=" N ALA B 646 " --> pdb=" O GLU B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 692 through 696 Processing sheet with id= A, first strand: chain 'B' and resid 591 through 593 removed outlier: 6.777A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN B 616 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER B 567 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B 618 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN B 652 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU B 619 " --> pdb=" O ASN B 652 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 654 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 621 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 656 " --> pdb=" O LEU B 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 5 through 8 Processing sheet with id= C, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.656A pdb=" N ARG C 39 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 558 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: 1.42 Time building geometry restraints manager: 2.35 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: 1949 1.34 - 1.46: 1020 1.46 - 1.58: 2922 1.58 - 1.70: 1 1.70 - 1.81: 38 Bond restraints: 5930 Sorted by residual: bond pdb=" C3R NMN A1001 " pdb=" C4R NMN A1001 " ideal model delta sigma weight residual 1.304 1.535 -0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C4R NMN A1001 " pdb=" O4R NMN A1001 " ideal model delta sigma weight residual 1.615 1.443 0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" C7 NMN A1001 " pdb=" N7 NMN A1001 " ideal model delta sigma weight residual 1.451 1.325 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C1R NMN A1001 " pdb=" O4R NMN A1001 " ideal model delta sigma weight residual 1.305 1.421 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C3R NMN A1001 " pdb=" O3R NMN A1001 " ideal model delta sigma weight residual 1.496 1.423 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 5925 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.48: 159 106.48 - 113.38: 3178 113.38 - 120.28: 2397 120.28 - 127.18: 2234 127.18 - 134.07: 58 Bond angle restraints: 8026 Sorted by residual: angle pdb=" N ALA A 102 " pdb=" CA ALA A 102 " pdb=" C ALA A 102 " ideal model delta sigma weight residual 113.18 107.98 5.20 1.21e+00 6.83e-01 1.85e+01 angle pdb=" CA LEU A 327 " pdb=" CB LEU A 327 " pdb=" CG LEU A 327 " ideal model delta sigma weight residual 116.30 131.02 -14.72 3.50e+00 8.16e-02 1.77e+01 angle pdb=" CA LYS A 80 " pdb=" CB LYS A 80 " pdb=" CG LYS A 80 " ideal model delta sigma weight residual 114.10 122.12 -8.02 2.00e+00 2.50e-01 1.61e+01 angle pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 112.89 107.93 4.96 1.24e+00 6.50e-01 1.60e+01 angle pdb=" N ARG A 110 " pdb=" CA ARG A 110 " pdb=" C ARG A 110 " ideal model delta sigma weight residual 111.56 105.58 5.98 1.53e+00 4.27e-01 1.53e+01 ... (remaining 8021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3229 17.82 - 35.63: 307 35.63 - 53.45: 46 53.45 - 71.26: 13 71.26 - 89.08: 6 Dihedral angle restraints: 3601 sinusoidal: 1458 harmonic: 2143 Sorted by residual: dihedral pdb=" CA ALA A 107 " pdb=" C ALA A 107 " pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA PRO B 623 " pdb=" C PRO B 623 " pdb=" N GLY B 624 " pdb=" CA GLY B 624 " ideal model delta harmonic sigma weight residual 180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.50 33.50 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 3598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 703 0.059 - 0.117: 173 0.117 - 0.176: 27 0.176 - 0.235: 9 0.235 - 0.293: 4 Chirality restraints: 916 Sorted by residual: chirality pdb=" CB VAL A 506 " pdb=" CA VAL A 506 " pdb=" CG1 VAL A 506 " pdb=" CG2 VAL A 506 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C1R NMN A1001 " pdb=" C2R NMN A1001 " pdb=" N1 NMN A1001 " pdb=" O4R NMN A1001 " both_signs ideal model delta sigma weight residual False 2.36 2.65 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 120 " pdb=" CA ILE A 120 " pdb=" CG1 ILE A 120 " pdb=" CG2 ILE A 120 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 913 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 107 " 0.019 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ALA A 107 " -0.069 2.00e-02 2.50e+03 pdb=" O ALA A 107 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL A 108 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 654 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO B 655 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 655 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 655 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 100 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C VAL C 100 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL C 100 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU C 101 " 0.018 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 58 2.56 - 3.15: 4556 3.15 - 3.73: 9045 3.73 - 4.32: 12308 4.32 - 4.90: 19954 Nonbonded interactions: 45921 Sorted by model distance: nonbonded pdb=" OE2 GLU A 264 " pdb=" CD2 LEU A 303 " model vdw 1.977 3.460 nonbonded pdb=" O LYS A 363 " pdb=" OG SER A 366 " model vdw 2.256 2.440 nonbonded pdb=" O SER A 485 " pdb=" OG SER A 485 " model vdw 2.320 2.440 nonbonded pdb=" O SER A 408 " pdb=" OG SER A 408 " model vdw 2.324 2.440 nonbonded pdb=" ND2 ASN B 652 " pdb=" O LEU B 699 " model vdw 2.326 2.520 ... (remaining 45916 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: 1.500 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: 0.000 Extract box with map and model: 6.700 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 19.600 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.231 5930 Z= 0.375 Angle : 1.042 14.721 8026 Z= 0.565 Chirality : 0.058 0.293 916 Planarity : 0.007 0.078 1040 Dihedral : 14.311 89.075 2214 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -3.32 (0.27), residues: 740 helix: -2.32 (0.22), residues: 370 sheet: -1.49 (0.55), residues: 64 loop : -2.00 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 103 HIS 0.004 0.001 HIS A 190 PHE 0.020 0.002 PHE A 308 TYR 0.018 0.002 TYR B 687 ARG 0.007 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ARG cc_start: 0.7620 (mmm160) cc_final: 0.7410 (mmt180) REVERT: A 391 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8408 (mtpp) REVERT: A 436 GLN cc_start: 0.8888 (mm110) cc_final: 0.8575 (mm-40) REVERT: A 464 LYS cc_start: 0.8803 (mttt) cc_final: 0.8538 (mtpt) REVERT: A 547 HIS cc_start: 0.6445 (t70) cc_final: 0.6238 (t70) REVERT: C 77 ASN cc_start: 0.8500 (m-40) cc_final: 0.8237 (m-40) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2213 time to fit residues: 54.4248 Evaluate side-chains 160 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.0070 chunk 56 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.0070 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 overall best weight: 0.0618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 190 HIS A 418 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5930 Z= 0.147 Angle : 0.638 8.926 8026 Z= 0.301 Chirality : 0.041 0.155 916 Planarity : 0.004 0.048 1040 Dihedral : 5.626 58.295 822 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.29 % Allowed : 12.72 % Favored : 85.99 % 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: -2.02 (0.29), residues: 740 helix: -1.26 (0.26), residues: 364 sheet: -0.96 (0.58), residues: 65 loop : -1.33 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 103 HIS 0.003 0.001 HIS A 190 PHE 0.014 0.001 PHE A 308 TYR 0.011 0.001 TYR B 687 ARG 0.008 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7107 (ptp-170) cc_final: 0.6849 (mpp80) REVERT: A 267 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7757 (mtm-85) REVERT: A 338 ARG cc_start: 0.7617 (mmm160) cc_final: 0.7411 (mmt180) REVERT: A 457 MET cc_start: 0.8251 (mtt) cc_final: 0.7969 (mtt) REVERT: A 547 HIS cc_start: 0.6298 (t70) cc_final: 0.6077 (t70) REVERT: C 65 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8400 (ttmm) outliers start: 8 outliers final: 6 residues processed: 182 average time/residue: 0.2425 time to fit residues: 54.1064 Evaluate side-chains 157 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 685 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5930 Z= 0.281 Angle : 0.654 8.335 8026 Z= 0.317 Chirality : 0.042 0.184 916 Planarity : 0.004 0.042 1040 Dihedral : 5.580 56.021 822 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.22 % Allowed : 15.78 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.30), residues: 740 helix: -0.82 (0.27), residues: 358 sheet: -1.09 (0.57), residues: 63 loop : -1.29 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 683 HIS 0.003 0.001 HIS A 190 PHE 0.027 0.002 PHE A 308 TYR 0.010 0.002 TYR C 95 ARG 0.010 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: C 65 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8392 (ttmm) outliers start: 20 outliers final: 16 residues processed: 164 average time/residue: 0.2344 time to fit residues: 47.3556 Evaluate side-chains 160 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 35 optimal weight: 0.0770 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5930 Z= 0.192 Angle : 0.606 9.369 8026 Z= 0.290 Chirality : 0.041 0.157 916 Planarity : 0.004 0.046 1040 Dihedral : 5.408 54.705 822 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.74 % Allowed : 17.39 % Favored : 79.87 % 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: -1.46 (0.30), residues: 740 helix: -0.70 (0.27), residues: 363 sheet: -1.21 (0.56), residues: 65 loop : -1.06 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 103 HIS 0.001 0.000 HIS A 190 PHE 0.027 0.001 PHE A 308 TYR 0.010 0.001 TYR C 80 ARG 0.012 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.662 Fit side-chains REVERT: A 191 MET cc_start: 0.7576 (tpp) cc_final: 0.7358 (tpt) REVERT: A 338 ARG cc_start: 0.7542 (mmm160) cc_final: 0.7072 (mmt180) REVERT: C 65 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8377 (ttmm) outliers start: 17 outliers final: 15 residues processed: 167 average time/residue: 0.2428 time to fit residues: 49.8752 Evaluate side-chains 165 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 666 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5930 Z= 0.283 Angle : 0.662 10.668 8026 Z= 0.320 Chirality : 0.042 0.158 916 Planarity : 0.004 0.051 1040 Dihedral : 5.454 53.409 822 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.54 % Allowed : 18.68 % Favored : 77.78 % 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: -1.18 (0.31), residues: 740 helix: -0.41 (0.28), residues: 344 sheet: -1.11 (0.56), residues: 63 loop : -0.97 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 103 HIS 0.003 0.001 HIS A 190 PHE 0.037 0.002 PHE A 308 TYR 0.010 0.002 TYR C 95 ARG 0.014 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.7711 (tpp) cc_final: 0.7474 (tpp) REVERT: A 451 LEU cc_start: 0.9225 (tp) cc_final: 0.9004 (tp) outliers start: 22 outliers final: 19 residues processed: 158 average time/residue: 0.2274 time to fit residues: 44.3325 Evaluate side-chains 162 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5930 Z= 0.196 Angle : 0.623 9.778 8026 Z= 0.300 Chirality : 0.041 0.150 916 Planarity : 0.004 0.066 1040 Dihedral : 5.334 53.264 822 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.06 % Allowed : 20.93 % Favored : 76.01 % 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: -1.11 (0.31), residues: 740 helix: -0.37 (0.28), residues: 350 sheet: -1.15 (0.55), residues: 65 loop : -0.91 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 103 HIS 0.002 0.000 HIS A 194 PHE 0.037 0.002 PHE A 308 TYR 0.010 0.001 TYR B 687 ARG 0.015 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 0.691 Fit side-chains REVERT: A 191 MET cc_start: 0.7706 (tpp) cc_final: 0.7422 (tpp) REVERT: A 268 LEU cc_start: 0.8753 (mt) cc_final: 0.8519 (mt) REVERT: A 308 PHE cc_start: 0.7154 (t80) cc_final: 0.6929 (t80) REVERT: A 451 LEU cc_start: 0.9196 (tp) cc_final: 0.8973 (tp) REVERT: A 510 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6324 (tp) REVERT: B 699 LEU cc_start: 0.7141 (mt) cc_final: 0.6352 (pp) outliers start: 19 outliers final: 17 residues processed: 160 average time/residue: 0.2297 time to fit residues: 45.7075 Evaluate side-chains 162 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 40 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 43 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5930 Z= 0.181 Angle : 0.631 9.149 8026 Z= 0.297 Chirality : 0.041 0.134 916 Planarity : 0.004 0.052 1040 Dihedral : 5.243 50.255 822 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.22 % Allowed : 21.26 % Favored : 75.52 % 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: -0.89 (0.31), residues: 740 helix: -0.16 (0.28), residues: 346 sheet: -1.12 (0.54), residues: 65 loop : -0.80 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 103 HIS 0.002 0.000 HIS A 190 PHE 0.026 0.002 PHE A 308 TYR 0.010 0.001 TYR B 687 ARG 0.010 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.698 Fit side-chains REVERT: A 191 MET cc_start: 0.7777 (tpp) cc_final: 0.7503 (tpp) REVERT: A 310 ARG cc_start: 0.7384 (mmm-85) cc_final: 0.6658 (tpp80) REVERT: B 699 LEU cc_start: 0.7043 (mt) cc_final: 0.6383 (pp) outliers start: 20 outliers final: 16 residues processed: 158 average time/residue: 0.2226 time to fit residues: 43.7407 Evaluate side-chains 158 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5930 Z= 0.203 Angle : 0.652 9.285 8026 Z= 0.309 Chirality : 0.041 0.143 916 Planarity : 0.004 0.043 1040 Dihedral : 5.296 51.736 822 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.22 % Allowed : 22.54 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.31), residues: 740 helix: -0.21 (0.28), residues: 349 sheet: -1.11 (0.55), residues: 65 loop : -0.66 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.003 0.000 HIS A 190 PHE 0.040 0.002 PHE A 308 TYR 0.010 0.001 TYR B 687 ARG 0.010 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.748 Fit side-chains REVERT: A 121 ARG cc_start: 0.6351 (tpt-90) cc_final: 0.5745 (tpp80) REVERT: A 191 MET cc_start: 0.7745 (tpp) cc_final: 0.7448 (tpp) REVERT: A 232 ASN cc_start: 0.7724 (t0) cc_final: 0.7099 (t0) REVERT: A 310 ARG cc_start: 0.7390 (mmm-85) cc_final: 0.6712 (tpp80) REVERT: B 699 LEU cc_start: 0.7136 (mt) cc_final: 0.6498 (pp) outliers start: 20 outliers final: 19 residues processed: 154 average time/residue: 0.2212 time to fit residues: 42.6030 Evaluate side-chains 161 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 0.0010 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5930 Z= 0.203 Angle : 0.659 8.611 8026 Z= 0.313 Chirality : 0.041 0.137 916 Planarity : 0.004 0.071 1040 Dihedral : 5.361 54.393 822 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.06 % Allowed : 23.51 % Favored : 73.43 % 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: -0.73 (0.31), residues: 740 helix: -0.06 (0.28), residues: 343 sheet: -1.15 (0.55), residues: 65 loop : -0.64 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 103 HIS 0.003 0.001 HIS A 190 PHE 0.053 0.002 PHE A 308 TYR 0.011 0.001 TYR A 213 ARG 0.019 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.685 Fit side-chains REVERT: A 121 ARG cc_start: 0.6384 (tpt-90) cc_final: 0.5777 (tpp80) REVERT: A 191 MET cc_start: 0.7699 (tpp) cc_final: 0.7451 (tpp) REVERT: A 232 ASN cc_start: 0.8078 (t0) cc_final: 0.7574 (t0) outliers start: 19 outliers final: 19 residues processed: 150 average time/residue: 0.2083 time to fit residues: 39.4134 Evaluate side-chains 158 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 chunk 67 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5930 Z= 0.205 Angle : 0.660 7.666 8026 Z= 0.315 Chirality : 0.041 0.138 916 Planarity : 0.005 0.082 1040 Dihedral : 5.406 54.676 822 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.38 % Allowed : 23.67 % Favored : 72.95 % 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: -0.70 (0.31), residues: 740 helix: -0.05 (0.28), residues: 343 sheet: -1.15 (0.55), residues: 65 loop : -0.61 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 103 HIS 0.003 0.001 HIS A 190 PHE 0.045 0.002 PHE A 308 TYR 0.010 0.001 TYR B 687 ARG 0.019 0.001 ARG A 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.625 Fit side-chains REVERT: A 121 ARG cc_start: 0.6414 (tpt-90) cc_final: 0.5813 (tpp80) REVERT: A 191 MET cc_start: 0.7699 (tpp) cc_final: 0.7466 (tpp) REVERT: A 232 ASN cc_start: 0.8107 (t0) cc_final: 0.7620 (t0) REVERT: A 451 LEU cc_start: 0.9180 (tp) cc_final: 0.8971 (tp) REVERT: B 616 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7179 (p0) outliers start: 21 outliers final: 18 residues processed: 151 average time/residue: 0.2054 time to fit residues: 39.0683 Evaluate side-chains 161 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 383 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.167660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137380 restraints weight = 10372.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136129 restraints weight = 15945.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136755 restraints weight = 14021.116| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5930 Z= 0.195 Angle : 0.652 7.732 8026 Z= 0.310 Chirality : 0.041 0.138 916 Planarity : 0.004 0.078 1040 Dihedral : 5.406 56.669 822 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.06 % Allowed : 23.99 % Favored : 72.95 % 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: -0.70 (0.31), residues: 740 helix: -0.08 (0.28), residues: 347 sheet: -1.16 (0.55), residues: 65 loop : -0.58 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.003 0.000 HIS A 190 PHE 0.043 0.002 PHE A 308 TYR 0.010 0.001 TYR B 687 ARG 0.018 0.001 ARG A 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.13 seconds wall clock time: 33 minutes 32.29 seconds (2012.29 seconds total)