Starting phenix.real_space_refine on Wed Jun 3 13:16:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vcb_64951/06_2026/9vcb_64951.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vcb_64951/06_2026/9vcb_64951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vcb_64951/06_2026/9vcb_64951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vcb_64951/06_2026/9vcb_64951.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vcb_64951/06_2026/9vcb_64951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vcb_64951/06_2026/9vcb_64951.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 sd= 0.133 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 7 5.49 5 S 23 5.16 5 C 3689 2.51 5 N 963 2.21 5 O 982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5665 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5520 Classifications: {'peptide': 705} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 667} Chain breaks: 2 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.50, per 1000 atoms: 0.26 Number of scatterers: 5665 At special positions: 0 Unit cell: (94.0695, 81.8958, 100.71, 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 23 16.00 P 7 15.00 O 982 8.00 N 963 7.00 C 3689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 636 " distance=2.11 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 312.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 682 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 580 " 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 56.5% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 171 through 185 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.996A pdb=" N VAL A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 247 Processing helix chain 'A' and resid 252 through 273 Processing helix chain 'A' and resid 276 through 295 Processing helix chain 'A' and resid 300 through 316 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.632A pdb=" N TRP A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 385 Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.622A pdb=" N LEU A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Proline residue: A 400 - end of helix Processing helix chain 'A' and resid 405 through 424 Processing helix chain 'A' and resid 428 through 451 Proline residue: A 440 - end of helix removed outlier: 4.317A pdb=" N GLY A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 577 through 582 Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 654 through 668 removed outlier: 3.972A pdb=" N MET A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 689 through 697 Processing helix chain 'A' and resid 715 through 724 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 759 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 84 removed outlier: 5.896A pdb=" N ILE A 79 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA A 95 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER A 91 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS A 108 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLY A 158 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG A 110 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL A 160 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR A 112 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS A 162 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N LYS A 114 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 12.440A pdb=" N GLU A 164 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY A 158 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS A 132 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 160 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 130 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 124 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 595 through 598 removed outlier: 9.443A pdb=" N GLN A 595 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP A 569 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 597 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 571 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY A 536 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N PHE A 572 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 538 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 612 through 615 removed outlier: 6.590A pdb=" N VAL A 637 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG A 646 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 678 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 648 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 677 " --> pdb=" O LEU A 702 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.72 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: 1000 1.32 - 1.46: 2067 1.46 - 1.59: 2704 1.59 - 1.72: 12 1.72 - 1.86: 39 Bond restraints: 5822 Sorted by residual: bond pdb=" C VAL A 701 " pdb=" O VAL A 701 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.04e-02 9.25e+03 1.80e+01 bond pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta sigma weight residual 1.528 1.467 0.062 1.56e-02 4.11e+03 1.58e+01 bond pdb=" C VAL A 75 " pdb=" O VAL A 75 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.07e-02 8.73e+03 1.37e+01 bond pdb=" CA SER A 62 " pdb=" CB SER A 62 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.63e-02 3.76e+03 1.36e+01 bond pdb=" CA SER A 9 " pdb=" CB SER A 9 " ideal model delta sigma weight residual 1.528 1.470 0.059 1.66e-02 3.63e+03 1.26e+01 ... (remaining 5817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 6806 1.96 - 3.91: 1061 3.91 - 5.86: 77 5.86 - 7.82: 5 7.82 - 9.77: 3 Bond angle restraints: 7952 Sorted by residual: angle pdb=" C ALA A 705 " pdb=" N GLY A 706 " pdb=" CA GLY A 706 " ideal model delta sigma weight residual 120.10 124.17 -4.07 9.50e-01 1.11e+00 1.84e+01 angle pdb=" CB ARG A 213 " pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " ideal model delta sigma weight residual 111.30 121.07 -9.77 2.30e+00 1.89e-01 1.81e+01 angle pdb=" N GLN A 39 " pdb=" CA GLN A 39 " pdb=" C GLN A 39 " ideal model delta sigma weight residual 112.23 107.09 5.14 1.26e+00 6.30e-01 1.67e+01 angle pdb=" C ILE A 771 " pdb=" N ASN A 772 " pdb=" CA ASN A 772 " ideal model delta sigma weight residual 123.46 118.32 5.14 1.35e+00 5.49e-01 1.45e+01 angle pdb=" CA ASP A 118 " pdb=" CB ASP A 118 " pdb=" CG ASP A 118 " ideal model delta sigma weight residual 112.60 116.32 -3.72 1.00e+00 1.00e+00 1.38e+01 ... (remaining 7947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3064 17.53 - 35.07: 280 35.07 - 52.60: 48 52.60 - 70.14: 17 70.14 - 87.67: 3 Dihedral angle restraints: 3412 sinusoidal: 1389 harmonic: 2023 Sorted by residual: dihedral pdb=" CA ASP A 745 " pdb=" C ASP A 745 " pdb=" N SER A 746 " pdb=" CA SER A 746 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLN A 524 " pdb=" C GLN A 524 " pdb=" N GLY A 525 " pdb=" CA GLY A 525 " ideal model delta harmonic sigma weight residual 180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY A 536 " pdb=" C GLY A 536 " pdb=" N LEU A 537 " pdb=" CA LEU A 537 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 435 0.047 - 0.093: 288 0.093 - 0.139: 138 0.139 - 0.186: 44 0.186 - 0.232: 8 Chirality restraints: 913 Sorted by residual: chirality pdb=" CB VAL A 749 " pdb=" CA VAL A 749 " pdb=" CG1 VAL A 749 " pdb=" CG2 VAL A 749 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL A 638 " pdb=" CA VAL A 638 " pdb=" CG1 VAL A 638 " pdb=" CG2 VAL A 638 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE A 597 " pdb=" CA ILE A 597 " pdb=" CG1 ILE A 597 " pdb=" CG2 ILE A 597 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 910 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 551 " 0.036 2.00e-02 2.50e+03 2.93e-02 1.71e+01 pdb=" CG TYR A 551 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 551 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 551 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 551 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 551 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 551 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR A 551 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 615 " 0.032 2.00e-02 2.50e+03 1.99e-02 9.88e+00 pdb=" CG TRP A 615 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 615 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 615 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 615 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 615 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 615 " -0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 615 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 615 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 615 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 647 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C VAL A 647 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL A 647 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 648 " 0.018 2.00e-02 2.50e+03 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 6 2.46 - 3.07: 3714 3.07 - 3.68: 8511 3.68 - 4.29: 13056 4.29 - 4.90: 21506 Nonbonded interactions: 46793 Sorted by model distance: nonbonded pdb=" OD2 ASP A 652 " pdb="ZN ZN A1000 " model vdw 1.853 2.230 nonbonded pdb=" OE2 GLU A 690 " pdb=" NH1 ARG A 725 " model vdw 2.310 3.120 nonbonded pdb=" O LYS A 660 " pdb=" OG1 THR A 663 " model vdw 2.370 3.040 nonbonded pdb=" NH1 ARG A 710 " pdb=" OH TYR A 711 " model vdw 2.404 3.120 nonbonded pdb=" OE1 GLU A 699 " pdb=" NH1 ARG A 747 " model vdw 2.404 3.120 ... (remaining 46788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.690 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.010 0.179 5825 Z= 0.636 Angle : 1.377 9.774 7954 Z= 0.919 Chirality : 0.072 0.232 913 Planarity : 0.010 0.099 965 Dihedral : 14.341 87.669 2105 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.72 % Favored : 97.00 % Rotamer: Outliers : 0.51 % Allowed : 3.22 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.28), residues: 699 helix: -0.45 (0.24), residues: 336 sheet: -0.22 (0.58), residues: 80 loop : -1.06 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG A 753 TYR 0.053 0.010 TYR A 551 PHE 0.037 0.008 PHE A 4 TRP 0.042 0.009 TRP A 515 HIS 0.012 0.004 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00971 / 0.62 ( 5822) covalent geometry : angle 1.37669 / 0.92 ( 7952) SS BOND : bond 0.07819 / 4.12 ( 1) SS BOND : angle 2.94261 / 1.68 ( 2) hydrogen bonds : bond 0.12928 / 8.86 ( 321) hydrogen bonds : angle 6.25059 / 4.38 ( 918) metal coordination : bond 0.17693 / 8.87 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.7442 (m-40) cc_final: 0.7070 (m110) REVERT: A 76 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7335 (ttm-80) REVERT: A 88 ASP cc_start: 0.7624 (m-30) cc_final: 0.7266 (p0) REVERT: A 159 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.6989 (ttm170) REVERT: A 169 GLN cc_start: 0.7420 (mt0) cc_final: 0.6640 (mm110) REVERT: A 188 GLN cc_start: 0.8013 (mt0) cc_final: 0.7184 (mp10) REVERT: A 189 GLN cc_start: 0.7081 (mp10) cc_final: 0.6362 (mp10) REVERT: A 207 GLU cc_start: 0.8323 (pm20) cc_final: 0.7882 (pt0) REVERT: A 232 THR cc_start: 0.7697 (m) cc_final: 0.7209 (p) REVERT: A 302 TRP cc_start: 0.6771 (m100) cc_final: 0.6443 (m-90) REVERT: A 411 MET cc_start: 0.6092 (ttp) cc_final: 0.5792 (ttp) REVERT: A 642 ASP cc_start: 0.6627 (t70) cc_final: 0.6350 (p0) REVERT: A 654 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 673 MET cc_start: 0.7854 (mtp) cc_final: 0.7072 (mmt) REVERT: A 697 SER cc_start: 0.8166 (t) cc_final: 0.7897 (m) REVERT: A 748 GLU cc_start: 0.8410 (tt0) cc_final: 0.7739 (tp30) REVERT: A 763 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7047 (mtt-85) outliers start: 3 outliers final: 1 residues processed: 100 average time/residue: 0.5147 time to fit residues: 54.0612 Evaluate side-chains 73 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108803 restraints weight = 6192.406| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.58 r_work: 0.3043 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.003 0.031 5825 Z= 0.140 Angle : 0.577 6.823 7954 Z= 0.304 Chirality : 0.041 0.147 913 Planarity : 0.004 0.045 965 Dihedral : 11.657 80.289 833 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.03 % Allowed : 7.80 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.30), residues: 699 helix: 1.47 (0.26), residues: 338 sheet: -0.12 (0.55), residues: 92 loop : -0.70 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 213 TYR 0.007 0.001 TYR A 38 PHE 0.016 0.002 PHE A 127 TRP 0.034 0.001 TRP A 370 HIS 0.007 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 5822) covalent geometry : angle 0.57658 / 0.30 ( 7952) SS BOND : bond 0.00166 / 0.09 ( 1) SS BOND : angle 0.85455 / 0.46 ( 2) hydrogen bonds : bond 0.04551 / 2.95 ( 321) hydrogen bonds : angle 4.75562 / 3.34 ( 918) metal coordination : bond 0.00053 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8175 (m-40) cc_final: 0.7906 (m110) REVERT: A 188 GLN cc_start: 0.8127 (mt0) cc_final: 0.7605 (mp-120) REVERT: A 189 GLN cc_start: 0.7877 (mp10) cc_final: 0.7417 (mp10) REVERT: A 302 TRP cc_start: 0.7666 (m100) cc_final: 0.7352 (m-90) REVERT: A 370 TRP cc_start: 0.5749 (p-90) cc_final: 0.5463 (p-90) REVERT: A 411 MET cc_start: 0.7956 (ttp) cc_final: 0.7499 (ttp) REVERT: A 659 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7600 (mpp) REVERT: A 668 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6785 (mp10) REVERT: A 673 MET cc_start: 0.8689 (mtp) cc_final: 0.8036 (mmt) outliers start: 12 outliers final: 4 residues processed: 81 average time/residue: 0.5744 time to fit residues: 48.6706 Evaluate side-chains 70 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 668 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107306 restraints weight = 6168.538| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.56 r_work: 0.3024 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5825 Z= 0.149 Angle : 0.558 6.395 7954 Z= 0.294 Chirality : 0.041 0.144 913 Planarity : 0.004 0.032 965 Dihedral : 11.365 82.350 832 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.22 % Allowed : 10.34 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.31), residues: 699 helix: 2.07 (0.27), residues: 338 sheet: -0.04 (0.52), residues: 92 loop : -0.78 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 763 TYR 0.007 0.001 TYR A 591 PHE 0.017 0.002 PHE A 127 TRP 0.028 0.001 TRP A 370 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 5822) covalent geometry : angle 0.55779 / 0.29 ( 7952) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 0.69540 / 0.39 ( 2) hydrogen bonds : bond 0.04291 / 2.79 ( 321) hydrogen bonds : angle 4.51539 / 3.16 ( 918) metal coordination : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.223 Fit side-chains REVERT: A 93 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: A 188 GLN cc_start: 0.8100 (mt0) cc_final: 0.7563 (mp-120) REVERT: A 189 GLN cc_start: 0.7914 (mp10) cc_final: 0.7458 (mp10) REVERT: A 214 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.7009 (tp-100) REVERT: A 302 TRP cc_start: 0.7713 (m100) cc_final: 0.7383 (m-90) REVERT: A 370 TRP cc_start: 0.5820 (p-90) cc_final: 0.5523 (p-90) REVERT: A 411 MET cc_start: 0.8143 (ttp) cc_final: 0.7676 (ttp) outliers start: 19 outliers final: 9 residues processed: 77 average time/residue: 0.4462 time to fit residues: 36.4634 Evaluate side-chains 71 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 641 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108256 restraints weight = 6228.050| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.56 r_work: 0.3035 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5825 Z= 0.122 Angle : 0.519 6.336 7954 Z= 0.273 Chirality : 0.040 0.141 913 Planarity : 0.004 0.031 965 Dihedral : 11.122 83.349 832 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.71 % Allowed : 11.53 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.31), residues: 699 helix: 2.33 (0.27), residues: 338 sheet: -0.02 (0.52), residues: 92 loop : -0.72 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 763 TYR 0.007 0.001 TYR A 711 PHE 0.017 0.001 PHE A 127 TRP 0.027 0.001 TRP A 370 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5822) covalent geometry : angle 0.51909 / 0.27 ( 7952) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 0.50669 / 0.27 ( 2) hydrogen bonds : bond 0.03871 / 2.51 ( 321) hydrogen bonds : angle 4.36713 / 3.04 ( 918) metal coordination : bond 0.00027 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.219 Fit side-chains REVERT: A 72 PRO cc_start: 0.8955 (Cg_exo) cc_final: 0.8748 (Cg_endo) REVERT: A 93 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: A 188 GLN cc_start: 0.8137 (mt0) cc_final: 0.7614 (mp10) REVERT: A 189 GLN cc_start: 0.7879 (mp10) cc_final: 0.7432 (mp10) REVERT: A 214 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.7041 (tp-100) REVERT: A 302 TRP cc_start: 0.7673 (m100) cc_final: 0.7344 (m-90) REVERT: A 370 TRP cc_start: 0.5796 (p-90) cc_final: 0.5461 (p-90) REVERT: A 396 MET cc_start: 0.8163 (tpp) cc_final: 0.7858 (mmm) REVERT: A 411 MET cc_start: 0.8144 (ttp) cc_final: 0.7691 (ttp) REVERT: A 668 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6204 (mp10) outliers start: 16 outliers final: 7 residues processed: 74 average time/residue: 0.4648 time to fit residues: 36.4603 Evaluate side-chains 73 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 668 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 68 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.108518 restraints weight = 6307.982| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.58 r_work: 0.3043 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5825 Z= 0.116 Angle : 0.511 6.188 7954 Z= 0.267 Chirality : 0.040 0.144 913 Planarity : 0.004 0.031 965 Dihedral : 10.958 84.465 832 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.39 % Allowed : 11.19 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.31), residues: 699 helix: 2.48 (0.27), residues: 338 sheet: -0.04 (0.52), residues: 92 loop : -0.68 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 763 TYR 0.006 0.001 TYR A 143 PHE 0.017 0.001 PHE A 127 TRP 0.026 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 5822) covalent geometry : angle 0.51081 / 0.27 ( 7952) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 0.41510 / 0.23 ( 2) hydrogen bonds : bond 0.03727 / 2.43 ( 321) hydrogen bonds : angle 4.27621 / 2.97 ( 918) metal coordination : bond 0.00030 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 72 PRO cc_start: 0.8930 (Cg_exo) cc_final: 0.8728 (Cg_endo) REVERT: A 93 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8282 (m-30) REVERT: A 188 GLN cc_start: 0.8137 (mt0) cc_final: 0.7613 (mp10) REVERT: A 189 GLN cc_start: 0.7873 (mp10) cc_final: 0.7476 (mp10) REVERT: A 213 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6166 (ttp-170) REVERT: A 214 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7162 (tp-100) REVERT: A 302 TRP cc_start: 0.7656 (m100) cc_final: 0.7381 (m-90) REVERT: A 370 TRP cc_start: 0.5438 (p-90) cc_final: 0.5225 (p-90) REVERT: A 411 MET cc_start: 0.8100 (ttp) cc_final: 0.7691 (ttp) outliers start: 20 outliers final: 8 residues processed: 79 average time/residue: 0.4531 time to fit residues: 37.9836 Evaluate side-chains 75 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 659 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106374 restraints weight = 6232.212| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.56 r_work: 0.3012 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5825 Z= 0.165 Angle : 0.558 6.164 7954 Z= 0.290 Chirality : 0.041 0.149 913 Planarity : 0.004 0.033 965 Dihedral : 11.087 84.954 832 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.39 % Allowed : 11.86 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.31), residues: 699 helix: 2.38 (0.27), residues: 338 sheet: -0.13 (0.51), residues: 93 loop : -0.72 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.007 0.001 TYR A 711 PHE 0.019 0.002 PHE A 127 TRP 0.026 0.001 TRP A 370 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 5822) covalent geometry : angle 0.55730 / 0.29 ( 7952) SS BOND : bond 0.00323 / 0.17 ( 1) SS BOND : angle 1.70125 / 0.90 ( 2) hydrogen bonds : bond 0.04179 / 2.73 ( 321) hydrogen bonds : angle 4.35723 / 3.02 ( 918) metal coordination : bond 0.00050 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.237 Fit side-chains REVERT: A 93 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: A 188 GLN cc_start: 0.8142 (mt0) cc_final: 0.7604 (mp-120) REVERT: A 189 GLN cc_start: 0.7971 (mp10) cc_final: 0.7539 (mp10) REVERT: A 213 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6232 (ttp-170) REVERT: A 214 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7207 (tp-100) REVERT: A 302 TRP cc_start: 0.7662 (m100) cc_final: 0.7377 (m-90) REVERT: A 370 TRP cc_start: 0.5435 (p-90) cc_final: 0.5172 (p-90) REVERT: A 411 MET cc_start: 0.8167 (ttp) cc_final: 0.7732 (ttp) REVERT: A 659 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7246 (mpp) outliers start: 20 outliers final: 10 residues processed: 79 average time/residue: 0.4444 time to fit residues: 37.1255 Evaluate side-chains 79 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 659 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 86 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106532 restraints weight = 6312.485| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.57 r_work: 0.3013 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5825 Z= 0.145 Angle : 0.539 6.208 7954 Z= 0.281 Chirality : 0.041 0.145 913 Planarity : 0.004 0.034 965 Dihedral : 11.050 84.979 832 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.56 % Allowed : 12.37 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.31), residues: 699 helix: 2.46 (0.27), residues: 338 sheet: -0.04 (0.51), residues: 92 loop : -0.77 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.006 0.001 TYR A 143 PHE 0.018 0.001 PHE A 127 TRP 0.026 0.001 TRP A 370 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 5822) covalent geometry : angle 0.53841 / 0.28 ( 7952) SS BOND : bond 0.00419 / 0.22 ( 1) SS BOND : angle 1.61995 / 0.85 ( 2) hydrogen bonds : bond 0.03962 / 2.59 ( 321) hydrogen bonds : angle 4.30796 / 2.98 ( 918) metal coordination : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 93 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: A 188 GLN cc_start: 0.8145 (mt0) cc_final: 0.7598 (mp-120) REVERT: A 189 GLN cc_start: 0.7962 (mp10) cc_final: 0.7557 (mp10) REVERT: A 213 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.6225 (ttp-170) REVERT: A 214 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7246 (tp-100) REVERT: A 302 TRP cc_start: 0.7679 (m100) cc_final: 0.7388 (m-90) REVERT: A 411 MET cc_start: 0.8172 (ttp) cc_final: 0.7739 (ttp) REVERT: A 743 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8036 (mtm-85) outliers start: 21 outliers final: 11 residues processed: 80 average time/residue: 0.4905 time to fit residues: 41.3821 Evaluate side-chains 81 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 743 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114618 restraints weight = 6481.163| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.71 r_work: 0.3180 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5825 Z= 0.138 Angle : 0.543 6.900 7954 Z= 0.281 Chirality : 0.041 0.144 913 Planarity : 0.004 0.033 965 Dihedral : 11.046 85.251 832 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.22 % Allowed : 13.22 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.31), residues: 699 helix: 2.47 (0.27), residues: 339 sheet: -0.04 (0.51), residues: 92 loop : -0.75 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 763 TYR 0.006 0.001 TYR A 143 PHE 0.018 0.001 PHE A 127 TRP 0.042 0.001 TRP A 370 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 5822) covalent geometry : angle 0.54269 / 0.28 ( 7952) SS BOND : bond 0.00331 / 0.17 ( 1) SS BOND : angle 1.17821 / 0.62 ( 2) hydrogen bonds : bond 0.03908 / 2.55 ( 321) hydrogen bonds : angle 4.28708 / 2.96 ( 918) metal coordination : bond 0.00041 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 93 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: A 188 GLN cc_start: 0.8114 (mt0) cc_final: 0.7519 (mp10) REVERT: A 189 GLN cc_start: 0.7919 (mp10) cc_final: 0.7490 (mp10) REVERT: A 213 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.6197 (ttp-170) REVERT: A 214 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7158 (tp-100) REVERT: A 239 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7815 (ttm) REVERT: A 302 TRP cc_start: 0.7617 (m100) cc_final: 0.7319 (m-90) REVERT: A 411 MET cc_start: 0.8072 (ttp) cc_final: 0.7624 (ttp) REVERT: A 743 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8022 (mtm-85) outliers start: 19 outliers final: 11 residues processed: 78 average time/residue: 0.4764 time to fit residues: 39.2192 Evaluate side-chains 80 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 743 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.0000 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 86 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115222 restraints weight = 6588.367| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.73 r_work: 0.3195 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5825 Z= 0.125 Angle : 0.535 7.376 7954 Z= 0.276 Chirality : 0.040 0.141 913 Planarity : 0.004 0.034 965 Dihedral : 11.020 85.578 832 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.39 % Allowed : 13.22 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.31), residues: 699 helix: 2.37 (0.27), residues: 345 sheet: -0.10 (0.51), residues: 93 loop : -0.72 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 763 TYR 0.006 0.001 TYR A 143 PHE 0.017 0.001 PHE A 127 TRP 0.058 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 5822) covalent geometry : angle 0.53476 / 0.28 ( 7952) SS BOND : bond 0.00303 / 0.16 ( 1) SS BOND : angle 1.13507 / 0.60 ( 2) hydrogen bonds : bond 0.03747 / 2.44 ( 321) hydrogen bonds : angle 4.24855 / 2.94 ( 918) metal coordination : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 188 GLN cc_start: 0.8116 (mt0) cc_final: 0.7524 (mp10) REVERT: A 189 GLN cc_start: 0.7920 (mp10) cc_final: 0.7502 (mp10) REVERT: A 214 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7145 (tp-100) REVERT: A 239 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7769 (ttm) REVERT: A 302 TRP cc_start: 0.7614 (m100) cc_final: 0.7317 (m-90) REVERT: A 411 MET cc_start: 0.8057 (ttp) cc_final: 0.7624 (ttp) REVERT: A 743 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8003 (mtm-85) outliers start: 20 outliers final: 12 residues processed: 76 average time/residue: 0.4818 time to fit residues: 38.6674 Evaluate side-chains 79 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 743 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 0.0030 chunk 3 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 47 optimal weight: 0.0370 chunk 11 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 overall best weight: 0.2868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 86 ASN A 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117645 restraints weight = 6698.738| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.74 r_work: 0.3226 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5825 Z= 0.102 Angle : 0.516 9.132 7954 Z= 0.266 Chirality : 0.040 0.136 913 Planarity : 0.004 0.034 965 Dihedral : 10.894 86.077 832 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.20 % Allowed : 14.58 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.32), residues: 699 helix: 2.44 (0.27), residues: 347 sheet: -0.07 (0.52), residues: 93 loop : -0.63 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 763 TYR 0.007 0.001 TYR A 143 PHE 0.018 0.001 PHE A 404 TRP 0.054 0.001 TRP A 370 HIS 0.003 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 5822) covalent geometry : angle 0.51614 / 0.27 ( 7952) SS BOND : bond 0.00259 / 0.14 ( 1) SS BOND : angle 0.92524 / 0.49 ( 2) hydrogen bonds : bond 0.03393 / 2.20 ( 321) hydrogen bonds : angle 4.15710 / 2.89 ( 918) metal coordination : bond 0.00021 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 188 GLN cc_start: 0.8064 (mt0) cc_final: 0.7535 (mp10) REVERT: A 189 GLN cc_start: 0.7944 (mp10) cc_final: 0.7532 (mp10) REVERT: A 214 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7093 (tp-100) REVERT: A 239 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7746 (ttm) REVERT: A 302 TRP cc_start: 0.7602 (m100) cc_final: 0.7312 (m-90) REVERT: A 411 MET cc_start: 0.8054 (ttp) cc_final: 0.7665 (ttp) outliers start: 13 outliers final: 8 residues processed: 74 average time/residue: 0.4718 time to fit residues: 36.9717 Evaluate side-chains 76 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 659 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 0.0370 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116597 restraints weight = 6604.117| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.73 r_work: 0.3211 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5825 Z= 0.114 Angle : 0.527 7.745 7954 Z= 0.272 Chirality : 0.040 0.140 913 Planarity : 0.004 0.033 965 Dihedral : 10.894 86.444 832 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.20 % Allowed : 14.75 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.32), residues: 699 helix: 2.50 (0.27), residues: 345 sheet: 0.04 (0.52), residues: 91 loop : -0.66 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 763 TYR 0.007 0.001 TYR A 143 PHE 0.017 0.001 PHE A 127 TRP 0.055 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 5822) covalent geometry : angle 0.52658 / 0.27 ( 7952) SS BOND : bond 0.00253 / 0.13 ( 1) SS BOND : angle 0.99476 / 0.52 ( 2) hydrogen bonds : bond 0.03528 / 2.29 ( 321) hydrogen bonds : angle 4.16567 / 2.89 ( 918) metal coordination : bond 0.00023 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.05 seconds wall clock time: 39 minutes 29.66 seconds (2369.66 seconds total)