Starting phenix.real_space_refine (version: dev) on Fri Feb 17 18:17:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/02_2023/8gni_34165_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/02_2023/8gni_34165.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/02_2023/8gni_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_34165/02_2023/8gni_34165_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/02_2023/8gni_34165_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/02_2023/8gni_34165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/02_2023/8gni_34165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/02_2023/8gni_34165_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gni_34165/02_2023/8gni_34165_updated.pdb" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 3.78, per 1000 atoms: 0.65 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: 2.09 Conformation dependent library (CDL) restraints added in 838.8 milliseconds 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: 0.68 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: 1.84 Time building geometry restraints manager: 2.28 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: 3228 17.82 - 35.63: 306 35.63 - 53.45: 43 53.45 - 71.26: 12 71.26 - 89.08: 6 Dihedral angle restraints: 3595 sinusoidal: 1452 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 3592 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 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. 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.920 Check model and map are aligned: 0.080 Process input model: 18.500 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 14.155 89.075 2208 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 % 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 *********************** 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 : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2297 time to fit residues: 56.4861 Evaluate side-chains 158 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9835 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.0070 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 overall best weight: 0.1814 ------------------------------------------------------------------------------- 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: 0.7479 moved from start: 0.1783 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= 0.155 Angle : 0.642 8.866 8026 Z= 0.306 Chirality : 0.041 0.159 916 Planarity : 0.004 0.048 1040 Dihedral : 4.838 55.923 816 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.77 % 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: -2.08 (0.29), residues: 740 helix: -1.28 (0.26), residues: 366 sheet: -0.94 (0.59), residues: 63 loop : -1.42 (0.35), residues: 311 *********************** 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 184 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 178 average time/residue: 0.2358 time to fit residues: 51.9776 Evaluate side-chains 158 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0573 time to fit residues: 1.9289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 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 190 HIS B 685 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2237 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= 0.267 Angle : 0.651 8.357 8026 Z= 0.317 Chirality : 0.042 0.158 916 Planarity : 0.004 0.044 1040 Dihedral : 4.884 51.802 816 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.13 % 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: -1.70 (0.30), residues: 740 helix: -0.86 (0.27), residues: 355 sheet: -1.16 (0.58), residues: 63 loop : -1.29 (0.35), residues: 322 *********************** 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 160 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 0.716 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 156 average time/residue: 0.2418 time to fit residues: 46.4282 Evaluate side-chains 146 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0612 time to fit residues: 1.4679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0010 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 35 optimal weight: 0.0030 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.1996 ------------------------------------------------------------------------------- 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: 0.7498 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 5930 Z= 0.156 Angle : 0.607 9.440 8026 Z= 0.287 Chirality : 0.040 0.159 916 Planarity : 0.004 0.039 1040 Dihedral : 4.652 51.354 816 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 1.29 % 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: -1.47 (0.30), residues: 740 helix: -0.71 (0.27), residues: 369 sheet: -1.18 (0.57), residues: 65 loop : -1.07 (0.37), residues: 306 *********************** 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 169 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 0.706 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 163 average time/residue: 0.2374 time to fit residues: 47.5419 Evaluate side-chains 156 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0554 time to fit residues: 1.4867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 0.0270 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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: 0.7544 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5930 Z= 0.234 Angle : 0.655 10.581 8026 Z= 0.311 Chirality : 0.041 0.151 916 Planarity : 0.004 0.037 1040 Dihedral : 4.630 46.008 816 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 2.09 % 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: -1.12 (0.30), residues: 740 helix: -0.41 (0.27), residues: 353 sheet: -1.08 (0.56), residues: 63 loop : -0.89 (0.36), residues: 324 *********************** 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 161 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.644 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 156 average time/residue: 0.2442 time to fit residues: 46.9333 Evaluate side-chains 150 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0590 time to fit residues: 1.9661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.0570 chunk 23 optimal weight: 0.0060 chunk 37 optimal weight: 0.5980 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** 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: 0.7509 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 5930 Z= 0.165 Angle : 0.635 9.579 8026 Z= 0.299 Chirality : 0.040 0.145 916 Planarity : 0.004 0.040 1040 Dihedral : 4.520 43.782 816 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.31), residues: 740 helix: -0.12 (0.28), residues: 342 sheet: -1.13 (0.56), residues: 65 loop : -0.66 (0.36), residues: 333 *********************** 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 159 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 0.649 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 157 average time/residue: 0.2291 time to fit residues: 44.5136 Evaluate side-chains 148 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0549 time to fit residues: 1.3449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 32 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 GLN ** 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: 0.7514 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5930 Z= 0.180 Angle : 0.640 9.369 8026 Z= 0.303 Chirality : 0.040 0.132 916 Planarity : 0.004 0.042 1040 Dihedral : 4.460 43.499 816 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 1.45 % 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: -0.65 (0.31), residues: 740 helix: 0.03 (0.28), residues: 341 sheet: -1.06 (0.55), residues: 65 loop : -0.65 (0.36), residues: 334 *********************** 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 156 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 0.676 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 150 average time/residue: 0.2374 time to fit residues: 44.1701 Evaluate side-chains 150 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0610 time to fit residues: 1.7310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 0.0060 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 HIS ** 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: 0.7537 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 5930 Z= 0.221 Angle : 0.667 10.119 8026 Z= 0.319 Chirality : 0.041 0.136 916 Planarity : 0.004 0.044 1040 Dihedral : 4.591 41.851 816 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.64 % 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: -0.66 (0.31), residues: 740 helix: -0.02 (0.28), residues: 346 sheet: -1.04 (0.55), residues: 65 loop : -0.61 (0.36), residues: 329 *********************** 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 149 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 0.655 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 147 average time/residue: 0.2386 time to fit residues: 43.3993 Evaluate side-chains 137 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0672 time to fit residues: 1.1677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 43 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.0692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7470 moved from start: 0.3401 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= 0.169 Angle : 0.671 9.117 8026 Z= 0.316 Chirality : 0.040 0.133 916 Planarity : 0.004 0.055 1040 Dihedral : 4.489 41.743 816 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.16 % 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: -0.48 (0.31), residues: 740 helix: 0.08 (0.29), residues: 341 sheet: -0.99 (0.57), residues: 65 loop : -0.44 (0.36), residues: 334 *********************** 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 151 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.649 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.2144 time to fit residues: 40.1793 Evaluate side-chains 139 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0537 time to fit residues: 0.9852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 5930 Z= 0.256 Angle : 0.715 10.876 8026 Z= 0.341 Chirality : 0.042 0.133 916 Planarity : 0.004 0.054 1040 Dihedral : 4.628 35.914 816 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.97 % 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: -0.61 (0.32), residues: 740 helix: -0.01 (0.28), residues: 359 sheet: -1.00 (0.56), residues: 65 loop : -0.56 (0.38), residues: 316 ********************** 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 146 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 0.537 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 141 average time/residue: 0.2106 time to fit residues: 37.6850 Evaluate side-chains 141 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0545 time to fit residues: 1.3532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 0.0050 chunk 16 optimal weight: 0.0570 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.0170 chunk 42 optimal weight: 0.9980 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.168353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137279 restraints weight = 10383.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138706 restraints weight = 15011.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139195 restraints weight = 9291.231| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 5930 Z= 0.196 Angle : 0.690 9.804 8026 Z= 0.329 Chirality : 0.041 0.144 916 Planarity : 0.004 0.054 1040 Dihedral : 4.571 35.606 816 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.48 % 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: -0.53 (0.31), residues: 740 helix: 0.04 (0.28), residues: 352 sheet: -1.00 (0.57), residues: 64 loop : -0.50 (0.37), residues: 324 =============================================================================== Job complete usr+sys time: 1787.06 seconds wall clock time: 32 minutes 52.82 seconds (1972.82 seconds total)