Starting phenix.real_space_refine on Sun Mar 10 22:48:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnx_26022/03_2024/7tnx_26022_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnx_26022/03_2024/7tnx_26022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnx_26022/03_2024/7tnx_26022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnx_26022/03_2024/7tnx_26022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnx_26022/03_2024/7tnx_26022_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnx_26022/03_2024/7tnx_26022_updated.pdb" } resolution = 3.54 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= 0.006 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 26 5.49 5 S 32 5.16 5 C 3581 2.51 5 N 976 2.21 5 O 1137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 435": "OD1" <-> "OD2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A ASP 763": "OD1" <-> "OD2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 883": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5753 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5234 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 265 Unusual residues: {'GTP': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 253 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 10} 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 4302 SG CYS A 810 24.961 51.835 20.300 1.00 32.46 S ATOM 4741 SG CYS A 864 25.057 50.376 16.542 1.00 45.36 S ATOM 4780 SG CYS A 869 26.399 53.639 17.338 1.00 48.58 S Time building chain proxies: 4.05, per 1000 atoms: 0.70 Number of scatterers: 5753 At special positions: 0 Unit cell: (88.2, 92.4, 82.95, 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 32 16.00 P 26 15.00 O 1137 8.00 N 976 7.00 C 3581 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: 2.33 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 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1242 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 6 sheets defined 44.7% alpha, 7.7% beta 10 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.840A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 4.065A 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 340 Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' 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 446 through 451 Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.349A 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 removed outlier: 3.578A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.830A pdb=" N GLN A 588 " --> pdb=" O GLN A 584 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.998A 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 639 through 648 removed outlier: 3.751A 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 840 removed outlier: 3.656A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing sheet with id= A, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.212A pdb=" N GLY A 407 " --> pdb=" O ILE A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 294 through 296 Processing sheet with id= C, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.877A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 893 through 895 removed outlier: 3.645A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= F, first strand: chain 'A' and resid 842 through 846 removed outlier: 3.562A pdb=" N GLU A 857 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A 878 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS A 876 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYS A 861 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A 874 " --> pdb=" O LYS A 861 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1673 1.33 - 1.45: 895 1.45 - 1.57: 3253 1.57 - 1.69: 49 1.69 - 1.82: 45 Bond restraints: 5915 Sorted by residual: bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.19e+01 bond pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.08e-02 8.57e+03 1.12e+01 bond pdb=" N VAL A 522 " pdb=" CA VAL A 522 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.09e-02 8.42e+03 1.01e+01 bond pdb=" N VAL A 453 " pdb=" CA VAL A 453 " ideal model delta sigma weight residual 1.460 1.485 -0.025 8.60e-03 1.35e+04 8.55e+00 bond pdb=" N VAL A 463 " pdb=" CA VAL A 463 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.11e-02 8.12e+03 8.10e+00 ... (remaining 5910 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.21: 257 106.21 - 113.21: 3156 113.21 - 120.21: 2520 120.21 - 127.21: 2079 127.21 - 134.21: 76 Bond angle restraints: 8088 Sorted by residual: angle pdb=" N VAL A 453 " pdb=" CA VAL A 453 " pdb=" C VAL A 453 " ideal model delta sigma weight residual 113.71 108.96 4.75 9.50e-01 1.11e+00 2.50e+01 angle pdb=" N THR A 881 " pdb=" CA THR A 881 " pdb=" C THR A 881 " ideal model delta sigma weight residual 114.56 108.88 5.68 1.27e+00 6.20e-01 2.00e+01 angle pdb=" N ARG A 728 " pdb=" CA ARG A 728 " pdb=" C ARG A 728 " ideal model delta sigma weight residual 114.04 108.87 5.17 1.24e+00 6.50e-01 1.74e+01 angle pdb=" N PHE A 789 " pdb=" CA PHE A 789 " pdb=" C PHE A 789 " ideal model delta sigma weight residual 110.97 107.09 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N ILE A 790 " pdb=" CA ILE A 790 " pdb=" C ILE A 790 " ideal model delta sigma weight residual 110.62 106.64 3.98 1.14e+00 7.69e-01 1.22e+01 ... (remaining 8083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.34: 3337 19.34 - 38.68: 225 38.68 - 58.02: 43 58.02 - 77.36: 31 77.36 - 96.70: 10 Dihedral angle restraints: 3646 sinusoidal: 1740 harmonic: 1906 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 7.90 96.70 1 2.00e+01 2.50e-03 2.68e+01 dihedral pdb=" CB GLU A 249 " pdb=" CG GLU A 249 " pdb=" CD GLU A 249 " pdb=" OE1 GLU A 249 " ideal model delta sinusoidal sigma weight residual 0.00 88.06 -88.06 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 503 " pdb=" CG GLU A 503 " pdb=" CD GLU A 503 " pdb=" OE1 GLU A 503 " ideal model delta sinusoidal sigma weight residual 0.00 -84.83 84.83 1 3.00e+01 1.11e-03 9.71e+00 ... (remaining 3643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 418 0.039 - 0.079: 264 0.079 - 0.118: 180 0.118 - 0.158: 52 0.158 - 0.197: 5 Chirality restraints: 919 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 2.63 -0.20 2.00e-01 2.50e+01 9.71e-01 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 2.61 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ILE A 790 " pdb=" N ILE A 790 " pdb=" C ILE A 790 " pdb=" CB ILE A 790 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 916 not shown) Planarity restraints: 943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 347 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C THR A 347 " -0.030 2.00e-02 2.50e+03 pdb=" O THR A 347 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 348 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 303 " -0.013 2.00e-02 2.50e+03 1.15e-02 2.67e+00 pdb=" CG TYR A 303 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 303 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 303 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 303 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 303 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 303 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 303 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 746 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C GLY A 746 " -0.025 2.00e-02 2.50e+03 pdb=" O GLY A 746 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL A 747 " 0.009 2.00e-02 2.50e+03 ... (remaining 940 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 738 2.78 - 3.31: 5904 3.31 - 3.84: 9273 3.84 - 4.37: 11290 4.37 - 4.90: 18368 Nonbonded interactions: 45573 Sorted by model distance: nonbonded pdb=" O2 U B 12 " pdb=" N2 G C 14 " model vdw 2.247 2.520 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.288 2.440 nonbonded pdb=" NH1 ARG A 811 " pdb=" O GLU A 890 " model vdw 2.321 2.520 nonbonded pdb=" OD1 ASN A 259 " pdb=" N VAL A 405 " model vdw 2.322 2.520 nonbonded pdb=" O ILE A 337 " pdb=" ND2 ASN A 341 " model vdw 2.394 2.520 ... (remaining 45568 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: 0.480 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: 1.860 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.100 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.011 0.045 5915 Z= 0.677 Angle : 1.082 7.703 8088 Z= 0.785 Chirality : 0.065 0.197 919 Planarity : 0.004 0.025 943 Dihedral : 15.461 96.698 2404 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.67 % Favored : 92.18 % Rotamer: Outliers : 0.17 % Allowed : 3.42 % Favored : 96.40 % 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: -2.75 (0.31), residues: 639 helix: -0.49 (0.29), residues: 294 sheet: -2.90 (0.51), residues: 72 loop : -3.04 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 873 HIS 0.012 0.002 HIS A 876 PHE 0.018 0.003 PHE A 853 TYR 0.021 0.004 TYR A 303 ARG 0.005 0.001 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.671 Fit side-chains REVERT: A 340 ASN cc_start: 0.8342 (m-40) cc_final: 0.8062 (m110) REVERT: A 369 MET cc_start: 0.7396 (mtt) cc_final: 0.7022 (mtp) REVERT: A 607 GLU cc_start: 0.8801 (tp30) cc_final: 0.7765 (mt-10) REVERT: A 635 LYS cc_start: 0.8489 (ttpt) cc_final: 0.7716 (ttmm) REVERT: A 715 TYR cc_start: 0.8385 (t80) cc_final: 0.7978 (t80) REVERT: A 716 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 867 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7594 (mm-40) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.2206 time to fit residues: 35.5598 Evaluate side-chains 90 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.0000 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.0570 chunk 59 optimal weight: 0.7980 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 762 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5915 Z= 0.143 Angle : 0.491 9.094 8088 Z= 0.239 Chirality : 0.037 0.218 919 Planarity : 0.003 0.033 943 Dihedral : 14.237 90.313 1063 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 1.71 % Allowed : 10.96 % Favored : 87.33 % 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: -1.36 (0.33), residues: 639 helix: 0.94 (0.30), residues: 294 sheet: -2.57 (0.54), residues: 72 loop : -2.58 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 771 HIS 0.003 0.001 HIS A 375 PHE 0.009 0.001 PHE A 460 TYR 0.008 0.001 TYR A 246 ARG 0.005 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.692 Fit side-chains REVERT: A 255 MET cc_start: 0.8691 (mtt) cc_final: 0.8151 (mtm) REVERT: A 369 MET cc_start: 0.7548 (mtt) cc_final: 0.7261 (mtp) REVERT: A 435 ASP cc_start: 0.7849 (t0) cc_final: 0.7612 (t0) REVERT: A 560 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8681 (ttt) REVERT: A 607 GLU cc_start: 0.8716 (tp30) cc_final: 0.7692 (mt-10) REVERT: A 635 LYS cc_start: 0.8519 (ttpt) cc_final: 0.7708 (ttmm) REVERT: A 715 TYR cc_start: 0.8490 (t80) cc_final: 0.8018 (t80) REVERT: A 716 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 867 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7663 (mm-40) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1919 time to fit residues: 24.0577 Evaluate side-chains 90 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.0010 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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: 0.7858 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5915 Z= 0.171 Angle : 0.506 9.794 8088 Z= 0.241 Chirality : 0.038 0.233 919 Planarity : 0.003 0.034 943 Dihedral : 14.103 91.248 1062 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.04 % Favored : 92.80 % Rotamer: Outliers : 2.57 % Allowed : 12.67 % Favored : 84.76 % 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: -0.67 (0.34), residues: 639 helix: 1.61 (0.31), residues: 293 sheet: -2.32 (0.58), residues: 72 loop : -2.30 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 873 HIS 0.003 0.001 HIS A 375 PHE 0.010 0.001 PHE A 459 TYR 0.010 0.001 TYR A 622 ARG 0.006 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.556 Fit side-chains REVERT: A 255 MET cc_start: 0.8853 (mtt) cc_final: 0.8472 (mtm) REVERT: A 346 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8536 (pp) REVERT: A 369 MET cc_start: 0.7694 (mtt) cc_final: 0.7396 (mtp) REVERT: A 435 ASP cc_start: 0.7966 (t0) cc_final: 0.7620 (t0) REVERT: A 607 GLU cc_start: 0.8777 (tp30) cc_final: 0.8452 (tp30) REVERT: A 635 LYS cc_start: 0.8666 (ttpt) cc_final: 0.7869 (ttmm) REVERT: A 641 ASP cc_start: 0.8104 (t0) cc_final: 0.7883 (t0) REVERT: A 715 TYR cc_start: 0.8557 (t80) cc_final: 0.8060 (t80) REVERT: A 716 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8158 (mm-30) REVERT: A 867 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7724 (mm-40) outliers start: 15 outliers final: 10 residues processed: 89 average time/residue: 0.1652 time to fit residues: 19.6569 Evaluate side-chains 87 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 762 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5915 Z= 0.180 Angle : 0.510 11.066 8088 Z= 0.242 Chirality : 0.038 0.197 919 Planarity : 0.003 0.035 943 Dihedral : 13.998 91.456 1062 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.73 % Favored : 93.11 % Rotamer: Outliers : 2.57 % Allowed : 13.87 % Favored : 83.56 % 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: -0.46 (0.35), residues: 639 helix: 1.77 (0.31), residues: 293 sheet: -2.12 (0.61), residues: 72 loop : -2.20 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 646 HIS 0.003 0.001 HIS A 871 PHE 0.010 0.001 PHE A 459 TYR 0.007 0.001 TYR A 622 ARG 0.007 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.635 Fit side-chains REVERT: A 255 MET cc_start: 0.8915 (mtt) cc_final: 0.8546 (mtm) REVERT: A 369 MET cc_start: 0.7734 (mtt) cc_final: 0.7430 (mtp) REVERT: A 591 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8550 (mm-30) REVERT: A 607 GLU cc_start: 0.8771 (tp30) cc_final: 0.8417 (tp30) REVERT: A 635 LYS cc_start: 0.8730 (ttpt) cc_final: 0.7953 (ttmm) REVERT: A 715 TYR cc_start: 0.8628 (t80) cc_final: 0.8135 (t80) REVERT: A 716 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 811 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.7911 (mmt90) REVERT: A 867 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7754 (mm-40) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.1612 time to fit residues: 19.7313 Evaluate side-chains 89 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.0030 chunk 26 optimal weight: 0.0980 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 overall best weight: 0.2588 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5915 Z= 0.120 Angle : 0.475 10.493 8088 Z= 0.226 Chirality : 0.037 0.185 919 Planarity : 0.003 0.032 943 Dihedral : 13.948 89.087 1062 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.90 % Rotamer: Outliers : 3.25 % Allowed : 15.58 % Favored : 81.16 % 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: -0.13 (0.35), residues: 639 helix: 2.00 (0.31), residues: 292 sheet: -2.16 (0.67), residues: 64 loop : -1.92 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 771 HIS 0.003 0.000 HIS A 375 PHE 0.007 0.001 PHE A 459 TYR 0.007 0.001 TYR A 313 ARG 0.005 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.676 Fit side-chains REVERT: A 255 MET cc_start: 0.8803 (mtt) cc_final: 0.8438 (mtm) REVERT: A 289 GLN cc_start: 0.8231 (mp10) cc_final: 0.7968 (mp10) REVERT: A 369 MET cc_start: 0.7602 (mtt) cc_final: 0.7302 (mtp) REVERT: A 435 ASP cc_start: 0.7930 (t0) cc_final: 0.7696 (t0) REVERT: A 591 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8455 (mm-30) REVERT: A 607 GLU cc_start: 0.8710 (tp30) cc_final: 0.8386 (tp30) REVERT: A 635 LYS cc_start: 0.8645 (ttpt) cc_final: 0.7832 (ttmm) REVERT: A 655 PHE cc_start: 0.9018 (p90) cc_final: 0.8758 (p90) REVERT: A 715 TYR cc_start: 0.8549 (t80) cc_final: 0.8212 (t80) REVERT: A 811 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7876 (mmt90) REVERT: A 867 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7734 (mm-40) outliers start: 19 outliers final: 13 residues processed: 97 average time/residue: 0.1667 time to fit residues: 21.7807 Evaluate side-chains 91 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5915 Z= 0.221 Angle : 0.549 10.632 8088 Z= 0.260 Chirality : 0.039 0.209 919 Planarity : 0.003 0.034 943 Dihedral : 13.881 91.632 1062 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.96 % Rotamer: Outliers : 2.57 % Allowed : 17.29 % Favored : 80.14 % 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: -0.25 (0.35), residues: 639 helix: 1.92 (0.31), residues: 288 sheet: -1.96 (0.62), residues: 74 loop : -1.98 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 873 HIS 0.004 0.001 HIS A 871 PHE 0.010 0.001 PHE A 295 TYR 0.007 0.001 TYR A 390 ARG 0.007 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.650 Fit side-chains REVERT: A 255 MET cc_start: 0.8868 (mtt) cc_final: 0.8536 (mtm) REVERT: A 369 MET cc_start: 0.7663 (mtt) cc_final: 0.7379 (mtp) REVERT: A 435 ASP cc_start: 0.7755 (t0) cc_final: 0.7454 (t0) REVERT: A 591 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8552 (mm-30) REVERT: A 607 GLU cc_start: 0.8733 (tp30) cc_final: 0.7797 (mt-10) REVERT: A 635 LYS cc_start: 0.8710 (ttpt) cc_final: 0.7918 (ttmm) REVERT: A 655 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8803 (p90) REVERT: A 715 TYR cc_start: 0.8629 (t80) cc_final: 0.8246 (t80) REVERT: A 867 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7845 (mm-40) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.1583 time to fit residues: 20.1442 Evaluate side-chains 95 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.0030 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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: 0.7866 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5915 Z= 0.147 Angle : 0.508 9.341 8088 Z= 0.241 Chirality : 0.038 0.212 919 Planarity : 0.003 0.033 943 Dihedral : 13.857 90.272 1062 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.42 % Favored : 93.43 % Rotamer: Outliers : 2.91 % Allowed : 16.78 % Favored : 80.31 % 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: -0.11 (0.35), residues: 639 helix: 2.05 (0.31), residues: 286 sheet: -1.89 (0.62), residues: 74 loop : -1.90 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 771 HIS 0.003 0.001 HIS A 375 PHE 0.007 0.001 PHE A 459 TYR 0.006 0.001 TYR A 390 ARG 0.007 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.644 Fit side-chains REVERT: A 255 MET cc_start: 0.8846 (mtt) cc_final: 0.8529 (mtm) REVERT: A 369 MET cc_start: 0.7559 (mtt) cc_final: 0.7281 (mtp) REVERT: A 562 ASP cc_start: 0.8184 (t0) cc_final: 0.7970 (t0) REVERT: A 591 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8465 (mm-30) REVERT: A 607 GLU cc_start: 0.8736 (tp30) cc_final: 0.7806 (mt-10) REVERT: A 635 LYS cc_start: 0.8701 (ttpt) cc_final: 0.7892 (ttmm) REVERT: A 715 TYR cc_start: 0.8620 (t80) cc_final: 0.8241 (t80) REVERT: A 802 ASP cc_start: 0.8183 (t70) cc_final: 0.7853 (t0) REVERT: A 811 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8006 (mmt90) REVERT: A 867 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7749 (mm-40) outliers start: 17 outliers final: 15 residues processed: 92 average time/residue: 0.1505 time to fit residues: 19.1612 Evaluate side-chains 96 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.0000 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.0370 chunk 60 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.2462 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5915 Z= 0.119 Angle : 0.487 7.965 8088 Z= 0.235 Chirality : 0.038 0.206 919 Planarity : 0.003 0.033 943 Dihedral : 13.836 88.619 1062 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.26 % Favored : 93.58 % Rotamer: Outliers : 2.57 % Allowed : 17.12 % Favored : 80.31 % 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: 0.11 (0.35), residues: 639 helix: 2.18 (0.31), residues: 288 sheet: -2.04 (0.67), residues: 64 loop : -1.71 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 771 HIS 0.003 0.000 HIS A 375 PHE 0.019 0.001 PHE A 655 TYR 0.013 0.001 TYR A 622 ARG 0.006 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.607 Fit side-chains REVERT: A 255 MET cc_start: 0.8808 (mtt) cc_final: 0.8432 (mtm) REVERT: A 369 MET cc_start: 0.7561 (mtt) cc_final: 0.7308 (mtp) REVERT: A 497 SER cc_start: 0.7680 (t) cc_final: 0.7458 (t) REVERT: A 562 ASP cc_start: 0.8158 (t0) cc_final: 0.7945 (t0) REVERT: A 591 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8477 (mm-30) REVERT: A 598 GLU cc_start: 0.8357 (tp30) cc_final: 0.8013 (tp30) REVERT: A 607 GLU cc_start: 0.8736 (tp30) cc_final: 0.7862 (mt-10) REVERT: A 635 LYS cc_start: 0.8638 (ttpt) cc_final: 0.7825 (ttmm) REVERT: A 715 TYR cc_start: 0.8569 (t80) cc_final: 0.8354 (t80) REVERT: A 802 ASP cc_start: 0.8183 (t70) cc_final: 0.7829 (t0) REVERT: A 811 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.7978 (mmt90) REVERT: A 867 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7741 (mm-40) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.1637 time to fit residues: 20.7907 Evaluate side-chains 93 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.0570 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 0.0040 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.5712 ------------------------------------------------------------------------------- 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: 0.7851 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5915 Z= 0.150 Angle : 0.505 7.706 8088 Z= 0.240 Chirality : 0.038 0.232 919 Planarity : 0.003 0.033 943 Dihedral : 13.780 89.673 1062 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.57 % Favored : 93.27 % Rotamer: Outliers : 2.40 % Allowed : 17.29 % Favored : 80.31 % 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: 0.16 (0.35), residues: 639 helix: 2.18 (0.31), residues: 286 sheet: -1.91 (0.69), residues: 64 loop : -1.63 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 771 HIS 0.003 0.000 HIS A 375 PHE 0.008 0.001 PHE A 655 TYR 0.014 0.001 TYR A 622 ARG 0.005 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.645 Fit side-chains REVERT: A 255 MET cc_start: 0.8849 (mtt) cc_final: 0.8508 (mtm) REVERT: A 369 MET cc_start: 0.7649 (mtt) cc_final: 0.7364 (mtp) REVERT: A 435 ASP cc_start: 0.7758 (t0) cc_final: 0.7500 (t0) REVERT: A 497 SER cc_start: 0.7696 (t) cc_final: 0.7492 (t) REVERT: A 562 ASP cc_start: 0.8211 (t0) cc_final: 0.7980 (t0) REVERT: A 591 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8480 (mm-30) REVERT: A 607 GLU cc_start: 0.8744 (tp30) cc_final: 0.7888 (mt-10) REVERT: A 635 LYS cc_start: 0.8686 (ttpt) cc_final: 0.7865 (ttmm) REVERT: A 715 TYR cc_start: 0.8587 (t80) cc_final: 0.8337 (t80) REVERT: A 802 ASP cc_start: 0.8147 (t70) cc_final: 0.7797 (t70) REVERT: A 811 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8039 (mmt90) outliers start: 14 outliers final: 13 residues processed: 87 average time/residue: 0.1603 time to fit residues: 19.0497 Evaluate side-chains 94 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.0270 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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: 0.7862 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5915 Z= 0.168 Angle : 0.523 7.673 8088 Z= 0.250 Chirality : 0.039 0.218 919 Planarity : 0.003 0.033 943 Dihedral : 13.754 90.000 1062 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.74 % Rotamer: Outliers : 2.57 % Allowed : 17.29 % Favored : 80.14 % 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: 0.04 (0.35), residues: 639 helix: 2.15 (0.31), residues: 286 sheet: -1.81 (0.61), residues: 74 loop : -1.80 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 873 HIS 0.003 0.000 HIS A 375 PHE 0.009 0.001 PHE A 655 TYR 0.012 0.001 TYR A 622 ARG 0.005 0.000 ARG A 859 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.619 Fit side-chains REVERT: A 255 MET cc_start: 0.8856 (mtt) cc_final: 0.8519 (mtm) REVERT: A 369 MET cc_start: 0.7645 (mtt) cc_final: 0.7358 (mtp) REVERT: A 435 ASP cc_start: 0.7737 (t0) cc_final: 0.7485 (t0) REVERT: A 562 ASP cc_start: 0.8201 (t0) cc_final: 0.7989 (t0) REVERT: A 591 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8485 (mm-30) REVERT: A 598 GLU cc_start: 0.8367 (tp30) cc_final: 0.8149 (tp30) REVERT: A 607 GLU cc_start: 0.8775 (tp30) cc_final: 0.7910 (mt-10) REVERT: A 635 LYS cc_start: 0.8680 (ttpt) cc_final: 0.7867 (ttmm) REVERT: A 715 TYR cc_start: 0.8615 (t80) cc_final: 0.8365 (t80) REVERT: A 802 ASP cc_start: 0.8091 (t70) cc_final: 0.7726 (t70) REVERT: A 811 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.7940 (mtt-85) outliers start: 15 outliers final: 14 residues processed: 87 average time/residue: 0.1645 time to fit residues: 19.4995 Evaluate side-chains 94 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.3114 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.138460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107681 restraints weight = 6694.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111338 restraints weight = 4284.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113910 restraints weight = 3195.678| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5915 Z= 0.140 Angle : 0.514 10.582 8088 Z= 0.245 Chirality : 0.038 0.214 919 Planarity : 0.003 0.032 943 Dihedral : 13.729 88.423 1062 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.57 % Allowed : 17.12 % Favored : 80.31 % 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: 0.17 (0.35), residues: 639 helix: 2.16 (0.31), residues: 285 sheet: -1.92 (0.67), residues: 64 loop : -1.57 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 771 HIS 0.003 0.000 HIS A 375 PHE 0.007 0.001 PHE A 655 TYR 0.011 0.001 TYR A 622 ARG 0.005 0.000 ARG A 859 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.25 seconds wall clock time: 26 minutes 56.39 seconds (1616.39 seconds total)