Starting phenix.real_space_refine on Tue Feb 13 11:01:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/02_2024/7to1_26026_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/02_2024/7to1_26026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/02_2024/7to1_26026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/02_2024/7to1_26026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/02_2024/7to1_26026_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/02_2024/7to1_26026_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 24 5.49 5 S 31 5.16 5 C 3492 2.51 5 N 947 2.21 5 O 1106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5601 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5123 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 477 Unusual residues: {'GTP': 1} Classifications: {'RNA': 21, 'undetermined': 1} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4191 SG CYS A 810 43.045 22.013 23.953 1.00 50.21 S ATOM 4630 SG CYS A 864 42.729 20.263 20.098 1.00 64.66 S ATOM 4669 SG CYS A 869 39.685 21.192 21.887 1.00 60.38 S Time building chain proxies: 3.83, per 1000 atoms: 0.68 Number of scatterers: 5601 At special positions: 0 Unit cell: (89.25, 94.5, 66.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 31 16.00 P 24 15.00 O 1106 8.00 N 947 7.00 C 3492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 5 sheets defined 44.4% alpha, 7.4% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.711A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 267 through 283 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 395 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 493 through 496 No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 507 through 522 removed outlier: 5.010A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 557 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.598A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 649 removed outlier: 4.382A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 770 Processing helix chain 'A' and resid 774 through 793 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 836 through 839 No H-bonds generated for 'chain 'A' and resid 836 through 839' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 294 through 296 Processing sheet with id= B, first strand: chain 'A' and resid 694 through 696 removed outlier: 3.586A pdb=" N LEU A 632 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 711 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE A 633 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 713 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A 737 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU A 714 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE A 739 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 893 through 895 removed outlier: 3.857A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= E, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.922A pdb=" N HIS A 876 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LYS A 861 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY A 874 " --> pdb=" O LYS A 861 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 603 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 895 1.32 - 1.44: 1579 1.44 - 1.57: 3195 1.57 - 1.69: 46 1.69 - 1.82: 43 Bond restraints: 5758 Sorted by residual: bond pdb=" C1' GTP B 1 " pdb=" C2' GTP B 1 " ideal model delta sigma weight residual 1.524 1.285 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1' GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C5 GTP B 1 " pdb=" C6 GTP B 1 " ideal model delta sigma weight residual 1.390 1.544 -0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" C4 GTP B 1 " pdb=" N3 GTP B 1 " ideal model delta sigma weight residual 1.355 1.490 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.64: 260 106.64 - 113.56: 3184 113.56 - 120.47: 2420 120.47 - 127.39: 1935 127.39 - 134.31: 73 Bond angle restraints: 7872 Sorted by residual: angle pdb=" CA GLY A 835 " pdb=" C GLY A 835 " pdb=" O GLY A 835 " ideal model delta sigma weight residual 121.41 118.49 2.92 8.80e-01 1.29e+00 1.10e+01 angle pdb=" C VAL A 453 " pdb=" N TYR A 454 " pdb=" CA TYR A 454 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CA VAL A 414 " pdb=" C VAL A 414 " pdb=" O VAL A 414 " ideal model delta sigma weight residual 120.34 117.52 2.82 9.10e-01 1.21e+00 9.62e+00 angle pdb=" N ILE A 489 " pdb=" CA ILE A 489 " pdb=" C ILE A 489 " ideal model delta sigma weight residual 113.53 110.85 2.68 9.80e-01 1.04e+00 7.50e+00 angle pdb=" C2' GTP B 1 " pdb=" C3' GTP B 1 " pdb=" C4' GTP B 1 " ideal model delta sigma weight residual 111.00 102.83 8.17 3.00e+00 1.11e-01 7.42e+00 ... (remaining 7867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.24: 3236 20.24 - 40.47: 228 40.47 - 60.70: 43 60.70 - 80.93: 26 80.93 - 101.17: 2 Dihedral angle restraints: 3535 sinusoidal: 1663 harmonic: 1872 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 3.43 101.17 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" C4' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " ideal model delta sinusoidal sigma weight residual -99.13 -165.63 66.50 1 2.00e+01 2.50e-03 1.44e+01 dihedral pdb=" CA LEU A 449 " pdb=" C LEU A 449 " pdb=" N GLU A 450 " pdb=" CA GLU A 450 " ideal model delta harmonic sigma weight residual -180.00 -161.31 -18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 411 0.041 - 0.081: 265 0.081 - 0.122: 188 0.122 - 0.162: 27 0.162 - 0.203: 2 Chirality restraints: 893 Sorted by residual: chirality pdb=" CA ILE A 360 " pdb=" N ILE A 360 " pdb=" C ILE A 360 " pdb=" CB ILE A 360 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE A 261 " pdb=" N ILE A 261 " pdb=" C ILE A 261 " pdb=" CB ILE A 261 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA ILE A 386 " pdb=" N ILE A 386 " pdb=" C ILE A 386 " pdb=" CB ILE A 386 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 890 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 62 " 0.028 2.00e-02 2.50e+03 1.31e-02 3.86e+00 pdb=" N1 U B 62 " -0.011 2.00e-02 2.50e+03 pdb=" C2 U B 62 " -0.010 2.00e-02 2.50e+03 pdb=" O2 U B 62 " -0.008 2.00e-02 2.50e+03 pdb=" N3 U B 62 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 62 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 62 " 0.014 2.00e-02 2.50e+03 pdb=" C5 U B 62 " -0.008 2.00e-02 2.50e+03 pdb=" C6 U B 62 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 697 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C THR A 697 " 0.021 2.00e-02 2.50e+03 pdb=" O THR A 697 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 698 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 60 " 0.017 2.00e-02 2.50e+03 6.79e-03 1.38e+00 pdb=" N9 G B 60 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G B 60 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G B 60 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 60 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 60 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 60 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 60 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 60 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 60 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G B 60 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G B 60 " -0.004 2.00e-02 2.50e+03 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1638 2.83 - 3.35: 5486 3.35 - 3.87: 9376 3.87 - 4.38: 10293 4.38 - 4.90: 17575 Nonbonded interactions: 44368 Sorted by model distance: nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.314 2.440 nonbonded pdb=" OH TYR A 622 " pdb=" OD1 ASN A 692 " model vdw 2.315 2.440 nonbonded pdb=" NH1 ARG A 811 " pdb=" O GLU A 890 " model vdw 2.336 2.520 nonbonded pdb=" O ILE A 337 " pdb=" ND2 ASN A 341 " model vdw 2.339 2.520 nonbonded pdb=" OG SER A 362 " pdb=" OG SER A 364 " model vdw 2.364 2.440 ... (remaining 44363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 1.850 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.300 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.012 0.239 5758 Z= 0.806 Angle : 1.047 8.173 7872 Z= 0.756 Chirality : 0.063 0.203 893 Planarity : 0.004 0.019 924 Dihedral : 15.282 101.166 2315 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % 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: -2.28 (0.31), residues: 627 helix: 0.24 (0.29), residues: 282 sheet: -3.75 (0.50), residues: 67 loop : -2.85 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 873 HIS 0.005 0.002 HIS A 782 PHE 0.016 0.003 PHE A 460 TYR 0.015 0.003 TYR A 390 ARG 0.008 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.9094 (mmtp) cc_final: 0.8600 (mptt) REVERT: A 287 GLN cc_start: 0.8710 (tp40) cc_final: 0.8243 (pm20) REVERT: A 298 ASN cc_start: 0.8024 (t0) cc_final: 0.7807 (t0) REVERT: A 373 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 388 PHE cc_start: 0.8300 (m-10) cc_final: 0.7722 (m-80) REVERT: A 481 ASP cc_start: 0.7314 (m-30) cc_final: 0.7111 (m-30) REVERT: A 525 MET cc_start: 0.7566 (mmt) cc_final: 0.7181 (mmp) REVERT: A 531 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8079 (tt0) REVERT: A 556 GLU cc_start: 0.7822 (tt0) cc_final: 0.7565 (mt-10) REVERT: A 598 GLU cc_start: 0.8597 (tp30) cc_final: 0.8378 (tp30) REVERT: A 603 ASP cc_start: 0.8437 (t0) cc_final: 0.7931 (t70) REVERT: A 773 GLU cc_start: 0.7947 (tt0) cc_final: 0.7544 (tm-30) REVERT: A 803 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8739 (mmmt) REVERT: A 907 LYS cc_start: 0.8642 (mttt) cc_final: 0.8119 (mtmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2366 time to fit residues: 38.3207 Evaluate side-chains 87 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 495 ASN A 517 GLN A 557 HIS A 595 GLN A 769 GLN A 784 GLN A 876 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5758 Z= 0.162 Angle : 0.507 7.828 7872 Z= 0.249 Chirality : 0.038 0.226 893 Planarity : 0.003 0.037 924 Dihedral : 13.638 89.502 1009 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.75 % Allowed : 12.96 % Favored : 85.29 % 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: -1.27 (0.34), residues: 627 helix: 1.23 (0.31), residues: 289 sheet: -3.32 (0.52), residues: 75 loop : -2.52 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 512 HIS 0.008 0.001 HIS A 280 PHE 0.008 0.001 PHE A 295 TYR 0.013 0.001 TYR A 622 ARG 0.007 0.001 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8459 (mtt) cc_final: 0.8257 (mtt) REVERT: A 256 LYS cc_start: 0.8945 (mmtp) cc_final: 0.8389 (mptt) REVERT: A 287 GLN cc_start: 0.8694 (tp40) cc_final: 0.8247 (pm20) REVERT: A 298 ASN cc_start: 0.8067 (t0) cc_final: 0.7841 (t0) REVERT: A 511 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 525 MET cc_start: 0.8087 (mmt) cc_final: 0.7803 (mmt) REVERT: A 531 GLU cc_start: 0.9041 (tm-30) cc_final: 0.7978 (tt0) REVERT: A 541 TYR cc_start: 0.8220 (m-80) cc_final: 0.7989 (m-80) REVERT: A 596 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 598 GLU cc_start: 0.8651 (tp30) cc_final: 0.8277 (tp30) REVERT: A 603 ASP cc_start: 0.8493 (t0) cc_final: 0.7983 (t70) REVERT: A 773 GLU cc_start: 0.7974 (tt0) cc_final: 0.7483 (tm-30) REVERT: A 803 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8727 (mmmt) REVERT: A 907 LYS cc_start: 0.8661 (mttt) cc_final: 0.8115 (mtmm) outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 0.1720 time to fit residues: 19.8888 Evaluate side-chains 81 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 890 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 876 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5758 Z= 0.166 Angle : 0.500 7.352 7872 Z= 0.245 Chirality : 0.038 0.182 893 Planarity : 0.003 0.034 924 Dihedral : 13.469 89.974 1009 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.63 % Allowed : 15.06 % Favored : 82.31 % 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: -0.80 (0.35), residues: 627 helix: 1.55 (0.31), residues: 289 sheet: -2.93 (0.59), residues: 68 loop : -2.29 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 646 HIS 0.004 0.001 HIS A 280 PHE 0.009 0.001 PHE A 295 TYR 0.012 0.001 TYR A 303 ARG 0.004 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 256 LYS cc_start: 0.8942 (mmtp) cc_final: 0.8388 (mptt) REVERT: A 287 GLN cc_start: 0.8682 (tp40) cc_final: 0.8265 (pm20) REVERT: A 511 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 525 MET cc_start: 0.8045 (mmt) cc_final: 0.7634 (mmp) REVERT: A 531 GLU cc_start: 0.8979 (tm-30) cc_final: 0.7975 (tt0) REVERT: A 541 TYR cc_start: 0.8223 (m-80) cc_final: 0.7967 (m-80) REVERT: A 596 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 598 GLU cc_start: 0.8648 (tp30) cc_final: 0.8225 (tp30) REVERT: A 603 ASP cc_start: 0.8489 (t0) cc_final: 0.7985 (t70) REVERT: A 773 GLU cc_start: 0.7996 (tt0) cc_final: 0.7583 (tm-30) REVERT: A 803 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8720 (mmmt) REVERT: A 907 LYS cc_start: 0.8694 (mttt) cc_final: 0.8243 (mtmm) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.1795 time to fit residues: 21.5969 Evaluate side-chains 85 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 890 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 overall best weight: 0.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5758 Z= 0.136 Angle : 0.484 7.187 7872 Z= 0.237 Chirality : 0.037 0.153 893 Planarity : 0.003 0.028 924 Dihedral : 13.428 89.265 1009 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.98 % Allowed : 16.11 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.35), residues: 627 helix: 1.84 (0.32), residues: 289 sheet: -2.67 (0.62), residues: 66 loop : -2.20 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 646 HIS 0.004 0.001 HIS A 280 PHE 0.009 0.001 PHE A 295 TYR 0.013 0.001 TYR A 303 ARG 0.004 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.8698 (tp40) cc_final: 0.8290 (pm20) REVERT: A 388 PHE cc_start: 0.8299 (m-10) cc_final: 0.7762 (m-80) REVERT: A 511 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 525 MET cc_start: 0.7984 (mmt) cc_final: 0.7602 (mmp) REVERT: A 531 GLU cc_start: 0.8969 (tm-30) cc_final: 0.7902 (tt0) REVERT: A 573 ASN cc_start: 0.8197 (t0) cc_final: 0.7606 (m-40) REVERT: A 598 GLU cc_start: 0.8632 (tp30) cc_final: 0.8211 (tp30) REVERT: A 603 ASP cc_start: 0.8554 (t0) cc_final: 0.8077 (t70) REVERT: A 773 GLU cc_start: 0.8038 (tt0) cc_final: 0.7622 (tm-30) REVERT: A 803 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8671 (mmmt) REVERT: A 889 ILE cc_start: 0.9186 (tp) cc_final: 0.8917 (tp) REVERT: A 907 LYS cc_start: 0.8687 (mttt) cc_final: 0.8248 (mtmm) outliers start: 17 outliers final: 11 residues processed: 94 average time/residue: 0.1734 time to fit residues: 21.5929 Evaluate side-chains 86 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5758 Z= 0.176 Angle : 0.508 7.587 7872 Z= 0.252 Chirality : 0.037 0.144 893 Planarity : 0.003 0.028 924 Dihedral : 13.338 89.353 1009 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.80 % Allowed : 17.51 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.35), residues: 627 helix: 1.99 (0.31), residues: 288 sheet: -2.47 (0.65), residues: 66 loop : -2.15 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 512 HIS 0.004 0.001 HIS A 280 PHE 0.010 0.001 PHE A 295 TYR 0.013 0.001 TYR A 622 ARG 0.003 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.8925 (mmtp) cc_final: 0.8388 (mptt) REVERT: A 287 GLN cc_start: 0.8674 (tp40) cc_final: 0.8297 (pm20) REVERT: A 388 PHE cc_start: 0.8344 (m-10) cc_final: 0.7805 (m-80) REVERT: A 495 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.6904 (t0) REVERT: A 511 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 525 MET cc_start: 0.8004 (mmt) cc_final: 0.7626 (mmp) REVERT: A 531 GLU cc_start: 0.9007 (tm-30) cc_final: 0.7887 (tt0) REVERT: A 598 GLU cc_start: 0.8608 (tp30) cc_final: 0.8154 (tp30) REVERT: A 603 ASP cc_start: 0.8567 (t0) cc_final: 0.8080 (t70) REVERT: A 773 GLU cc_start: 0.8052 (tt0) cc_final: 0.7636 (tm-30) REVERT: A 803 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8690 (mmmt) REVERT: A 907 LYS cc_start: 0.8647 (mttt) cc_final: 0.8169 (mtmm) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 0.1882 time to fit residues: 23.3903 Evaluate side-chains 86 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 62 optimal weight: 0.0980 chunk 52 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5758 Z= 0.126 Angle : 0.488 7.123 7872 Z= 0.239 Chirality : 0.037 0.176 893 Planarity : 0.003 0.029 924 Dihedral : 13.373 88.671 1009 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.63 % Allowed : 18.39 % Favored : 78.98 % 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: -0.18 (0.35), residues: 627 helix: 2.13 (0.31), residues: 289 sheet: -2.34 (0.62), residues: 77 loop : -2.11 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 646 HIS 0.002 0.001 HIS A 280 PHE 0.008 0.001 PHE A 295 TYR 0.014 0.001 TYR A 303 ARG 0.003 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.8606 (tp40) cc_final: 0.8263 (pm20) REVERT: A 388 PHE cc_start: 0.8298 (m-10) cc_final: 0.7752 (m-80) REVERT: A 495 ASN cc_start: 0.7254 (OUTLIER) cc_final: 0.6937 (t0) REVERT: A 511 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7838 (tm-30) REVERT: A 525 MET cc_start: 0.8013 (mmt) cc_final: 0.7697 (mmp) REVERT: A 531 GLU cc_start: 0.8990 (tm-30) cc_final: 0.7906 (tt0) REVERT: A 598 GLU cc_start: 0.8609 (tp30) cc_final: 0.8147 (tp30) REVERT: A 603 ASP cc_start: 0.8586 (t0) cc_final: 0.8110 (t70) REVERT: A 760 MET cc_start: 0.8170 (ttp) cc_final: 0.7844 (ttp) REVERT: A 773 GLU cc_start: 0.7974 (tt0) cc_final: 0.7559 (tm-30) REVERT: A 803 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8692 (mmmt) REVERT: A 907 LYS cc_start: 0.8641 (mttt) cc_final: 0.8092 (mtmm) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.1739 time to fit residues: 22.4315 Evaluate side-chains 88 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5758 Z= 0.161 Angle : 0.524 9.019 7872 Z= 0.254 Chirality : 0.039 0.353 893 Planarity : 0.003 0.028 924 Dihedral : 13.279 88.677 1009 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.80 % Allowed : 19.79 % Favored : 77.41 % 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: -0.08 (0.36), residues: 627 helix: 2.22 (0.31), residues: 288 sheet: -2.38 (0.62), residues: 79 loop : -2.00 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.003 0.001 HIS A 280 PHE 0.009 0.001 PHE A 295 TYR 0.012 0.001 TYR A 303 ARG 0.003 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.8749 (tp40) cc_final: 0.8385 (pm20) REVERT: A 346 LEU cc_start: 0.8945 (pt) cc_final: 0.8638 (pt) REVERT: A 388 PHE cc_start: 0.8312 (m-10) cc_final: 0.7758 (m-80) REVERT: A 495 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.6950 (t0) REVERT: A 511 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 525 MET cc_start: 0.7896 (mmt) cc_final: 0.7594 (mmp) REVERT: A 531 GLU cc_start: 0.9010 (tm-30) cc_final: 0.7886 (tt0) REVERT: A 598 GLU cc_start: 0.8632 (tp30) cc_final: 0.8193 (tp30) REVERT: A 603 ASP cc_start: 0.8630 (t0) cc_final: 0.8124 (t70) REVERT: A 760 MET cc_start: 0.8208 (ttp) cc_final: 0.7928 (ttp) REVERT: A 773 GLU cc_start: 0.7995 (tt0) cc_final: 0.7607 (tm-30) REVERT: A 803 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8699 (mmmt) REVERT: A 907 LYS cc_start: 0.8640 (mttt) cc_final: 0.8077 (mtmm) outliers start: 16 outliers final: 14 residues processed: 88 average time/residue: 0.1897 time to fit residues: 21.9169 Evaluate side-chains 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5758 Z= 0.244 Angle : 0.573 8.550 7872 Z= 0.280 Chirality : 0.041 0.344 893 Planarity : 0.003 0.027 924 Dihedral : 13.245 88.965 1009 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.80 % Allowed : 19.79 % Favored : 77.41 % 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: -0.21 (0.36), residues: 627 helix: 2.01 (0.31), residues: 290 sheet: -2.38 (0.61), residues: 77 loop : -2.00 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 646 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE A 295 TYR 0.018 0.001 TYR A 622 ARG 0.004 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.8750 (tp40) cc_final: 0.8367 (pm20) REVERT: A 388 PHE cc_start: 0.8407 (m-10) cc_final: 0.7883 (m-80) REVERT: A 495 ASN cc_start: 0.7269 (t160) cc_final: 0.6947 (t0) REVERT: A 511 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 598 GLU cc_start: 0.8606 (tp30) cc_final: 0.8210 (tp30) REVERT: A 603 ASP cc_start: 0.8605 (t0) cc_final: 0.8140 (t70) REVERT: A 773 GLU cc_start: 0.8032 (tt0) cc_final: 0.7633 (tm-30) REVERT: A 811 ARG cc_start: 0.7798 (mmt180) cc_final: 0.7379 (mmt90) REVERT: A 896 ASP cc_start: 0.8485 (m-30) cc_final: 0.8263 (m-30) REVERT: A 907 LYS cc_start: 0.8629 (mttt) cc_final: 0.8129 (mtmm) outliers start: 16 outliers final: 14 residues processed: 87 average time/residue: 0.1783 time to fit residues: 20.6972 Evaluate side-chains 86 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5758 Z= 0.161 Angle : 0.547 12.097 7872 Z= 0.262 Chirality : 0.040 0.379 893 Planarity : 0.003 0.031 924 Dihedral : 13.293 88.532 1009 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.45 % Allowed : 19.79 % Favored : 77.76 % 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: 0.03 (0.36), residues: 627 helix: 2.17 (0.31), residues: 291 sheet: -2.10 (0.66), residues: 71 loop : -1.91 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.004 0.001 HIS A 280 PHE 0.008 0.001 PHE A 295 TYR 0.015 0.001 TYR A 303 ARG 0.002 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.8757 (tp40) cc_final: 0.8393 (pm20) REVERT: A 346 LEU cc_start: 0.8951 (pt) cc_final: 0.8660 (pt) REVERT: A 388 PHE cc_start: 0.8340 (m-10) cc_final: 0.7806 (m-80) REVERT: A 495 ASN cc_start: 0.7252 (t160) cc_final: 0.6957 (t0) REVERT: A 511 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 598 GLU cc_start: 0.8580 (tp30) cc_final: 0.8177 (tp30) REVERT: A 603 ASP cc_start: 0.8622 (t0) cc_final: 0.8104 (t70) REVERT: A 773 GLU cc_start: 0.7939 (tt0) cc_final: 0.7595 (tm-30) REVERT: A 811 ARG cc_start: 0.7705 (mmt180) cc_final: 0.7270 (mmt90) REVERT: A 907 LYS cc_start: 0.8533 (mttt) cc_final: 0.8012 (mtmm) outliers start: 14 outliers final: 13 residues processed: 94 average time/residue: 0.1660 time to fit residues: 20.9927 Evaluate side-chains 89 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5758 Z= 0.199 Angle : 0.572 11.570 7872 Z= 0.277 Chirality : 0.041 0.379 893 Planarity : 0.003 0.029 924 Dihedral : 13.257 89.098 1009 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.45 % Allowed : 21.02 % Favored : 76.53 % 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: 0.03 (0.36), residues: 627 helix: 2.10 (0.31), residues: 291 sheet: -2.10 (0.66), residues: 71 loop : -1.83 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 646 HIS 0.004 0.001 HIS A 280 PHE 0.010 0.001 PHE A 295 TYR 0.015 0.001 TYR A 622 ARG 0.003 0.000 ARG A 811 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.8764 (tp40) cc_final: 0.8404 (pm20) REVERT: A 388 PHE cc_start: 0.8350 (m-10) cc_final: 0.7823 (m-80) REVERT: A 495 ASN cc_start: 0.7258 (t160) cc_final: 0.6970 (t0) REVERT: A 511 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 598 GLU cc_start: 0.8613 (tp30) cc_final: 0.8231 (tp30) REVERT: A 603 ASP cc_start: 0.8615 (t0) cc_final: 0.8163 (t70) REVERT: A 773 GLU cc_start: 0.7947 (tt0) cc_final: 0.7604 (tm-30) REVERT: A 811 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7299 (mmt90) REVERT: A 907 LYS cc_start: 0.8562 (mttt) cc_final: 0.8017 (mtmm) outliers start: 14 outliers final: 14 residues processed: 93 average time/residue: 0.1698 time to fit residues: 20.9545 Evaluate side-chains 95 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.153732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128636 restraints weight = 6391.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131066 restraints weight = 4576.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132504 restraints weight = 3996.645| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5758 Z= 0.169 Angle : 0.553 11.680 7872 Z= 0.269 Chirality : 0.040 0.377 893 Planarity : 0.003 0.028 924 Dihedral : 13.278 88.723 1009 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.98 % Allowed : 20.14 % Favored : 76.88 % 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: 0.06 (0.36), residues: 627 helix: 2.15 (0.31), residues: 291 sheet: -2.20 (0.64), residues: 73 loop : -1.80 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 646 HIS 0.002 0.000 HIS A 381 PHE 0.008 0.001 PHE A 295 TYR 0.017 0.001 TYR A 541 ARG 0.002 0.000 ARG A 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1390.52 seconds wall clock time: 25 minutes 57.51 seconds (1557.51 seconds total)