Starting phenix.real_space_refine on Wed Jan 15 01:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r34_18860/01_2025/8r34_18860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r34_18860/01_2025/8r34_18860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r34_18860/01_2025/8r34_18860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r34_18860/01_2025/8r34_18860.map" model { file = "/net/cci-nas-00/data/ceres_data/8r34_18860/01_2025/8r34_18860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r34_18860/01_2025/8r34_18860.cif" } resolution = 2.62 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= 0.075 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 P 10 5.49 5 S 52 5.16 5 Na 4 4.78 5 C 5174 2.51 5 N 1136 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7762 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3651 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 1 Chain: "B" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3651 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 1 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 199 Unusual residues: {' NA': 2, '3PH': 4, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 199 Unusual residues: {' NA': 2, '3PH': 4, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 5.76, per 1000 atoms: 0.74 Number of scatterers: 7762 At special positions: 0 Unit cell: (93.725, 93.725, 74.98, 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) S 52 16.00 P 10 15.00 Na 4 11.00 O 1386 8.00 N 1136 7.00 C 5174 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 - 3.00 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: 2.34 Conformation dependent library (CDL) restraints added in 954.4 milliseconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.662A pdb=" N PHE A 409 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 430 Processing helix chain 'A' and resid 435 through 455 removed outlier: 3.592A pdb=" N ALA A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.634A pdb=" N ALA A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.506A pdb=" N TYR A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 533 removed outlier: 3.739A pdb=" N TRP A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 555 removed outlier: 3.751A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 578 through 596 Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 646 removed outlier: 3.509A pdb=" N VAL A 626 " --> pdb=" O GLN A 622 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 664 through 683 Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.564A pdb=" N ILE A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 707 removed outlier: 3.903A pdb=" N ILE A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 Processing helix chain 'A' and resid 720 through 741 removed outlier: 3.568A pdb=" N VAL A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 removed outlier: 3.804A pdb=" N LYS A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 755 " --> pdb=" O GLN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 775 removed outlier: 3.699A pdb=" N THR A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 796 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 801 through 814 Processing helix chain 'A' and resid 824 through 832 removed outlier: 3.545A pdb=" N SER A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 852 removed outlier: 3.566A pdb=" N VAL A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 874 removed outlier: 3.919A pdb=" N VAL A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.707A pdb=" N PHE B 409 " --> pdb=" O PRO B 406 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 410 " --> pdb=" O LYS B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 411 through 430 Processing helix chain 'B' and resid 435 through 455 removed outlier: 3.592A pdb=" N ALA B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 473 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 485 through 496 removed outlier: 3.651A pdb=" N ALA B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 518 Processing helix chain 'B' and resid 519 through 533 removed outlier: 3.523A pdb=" N SER B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP B 527 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 555 removed outlier: 3.749A pdb=" N TRP B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 567 Processing helix chain 'B' and resid 567 through 572 Processing helix chain 'B' and resid 578 through 596 Processing helix chain 'B' and resid 603 through 614 Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 619 through 646 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 664 through 683 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.573A pdb=" N ILE B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 707 removed outlier: 3.901A pdb=" N ILE B 702 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'B' and resid 720 through 741 removed outlier: 3.575A pdb=" N VAL B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 removed outlier: 3.754A pdb=" N LYS B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 775 removed outlier: 3.723A pdb=" N THR B 775 " --> pdb=" O LEU B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 796 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 801 through 814 Processing helix chain 'B' and resid 824 through 832 removed outlier: 3.565A pdb=" N SER B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 852 removed outlier: 3.553A pdb=" N VAL B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 874 removed outlier: 3.881A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B 872 " --> pdb=" O GLY B 868 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1524 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: 2.39 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1168 1.33 - 1.45: 1899 1.45 - 1.57: 4685 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7846 Sorted by residual: bond pdb=" O3 PO4 B 902 " pdb=" P PO4 B 902 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" O3 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O4 PO4 B 902 " pdb=" P PO4 B 902 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O4 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" O2 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.39e+00 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 9900 1.12 - 2.24: 534 2.24 - 3.36: 86 3.36 - 4.49: 35 4.49 - 5.61: 19 Bond angle restraints: 10574 Sorted by residual: angle pdb=" C PHE A 656 " pdb=" N LYS A 657 " pdb=" CA LYS A 657 " ideal model delta sigma weight residual 121.61 127.22 -5.61 1.39e+00 5.18e-01 1.63e+01 angle pdb=" C ILE A 786 " pdb=" N ILE A 787 " pdb=" CA ILE A 787 " ideal model delta sigma weight residual 120.24 122.76 -2.52 6.30e-01 2.52e+00 1.60e+01 angle pdb=" C ILE B 786 " pdb=" N ILE B 787 " pdb=" CA ILE B 787 " ideal model delta sigma weight residual 120.24 122.54 -2.30 6.30e-01 2.52e+00 1.34e+01 angle pdb=" C ILE A 699 " pdb=" N ILE A 700 " pdb=" CA ILE A 700 " ideal model delta sigma weight residual 120.33 123.20 -2.87 8.00e-01 1.56e+00 1.29e+01 angle pdb=" C ILE B 699 " pdb=" N ILE B 700 " pdb=" CA ILE B 700 " ideal model delta sigma weight residual 120.33 123.07 -2.74 8.00e-01 1.56e+00 1.17e+01 ... (remaining 10569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3923 17.40 - 34.80: 543 34.80 - 52.19: 193 52.19 - 69.59: 78 69.59 - 86.99: 11 Dihedral angle restraints: 4748 sinusoidal: 1966 harmonic: 2782 Sorted by residual: dihedral pdb=" CA GLU A 755 " pdb=" C GLU A 755 " pdb=" N ASN A 756 " pdb=" CA ASN A 756 " ideal model delta harmonic sigma weight residual 180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CG ARG A 850 " pdb=" CD ARG A 850 " pdb=" NE ARG A 850 " pdb=" CZ ARG A 850 " ideal model delta sinusoidal sigma weight residual 180.00 -136.60 -43.40 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA LYS A 735 " pdb=" CB LYS A 735 " pdb=" CG LYS A 735 " pdb=" CD LYS A 735 " ideal model delta sinusoidal sigma weight residual -180.00 -120.22 -59.78 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 786 0.033 - 0.066: 357 0.066 - 0.099: 97 0.099 - 0.132: 20 0.132 - 0.164: 2 Chirality restraints: 1262 Sorted by residual: chirality pdb=" CG LEU A 408 " pdb=" CB LEU A 408 " pdb=" CD1 LEU A 408 " pdb=" CD2 LEU A 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CG LEU B 408 " pdb=" CB LEU B 408 " pdb=" CD1 LEU B 408 " pdb=" CD2 LEU B 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ASN A 756 " pdb=" N ASN A 756 " pdb=" C ASN A 756 " pdb=" CB ASN A 756 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1259 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 719 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO B 720 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 720 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 720 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 643 " 0.013 2.00e-02 2.50e+03 1.29e-02 2.91e+00 pdb=" CG PHE B 643 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 643 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 643 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 643 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 643 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 643 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 719 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 720 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 720 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 720 " -0.023 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 260 2.71 - 3.26: 7715 3.26 - 3.81: 12757 3.81 - 4.35: 17570 4.35 - 4.90: 28579 Nonbonded interactions: 66881 Sorted by model distance: nonbonded pdb=" O LEU B 860 " pdb=" OG1 THR B 864 " model vdw 2.167 3.040 nonbonded pdb=" O LEU A 860 " pdb=" OG1 THR A 864 " model vdw 2.202 3.040 nonbonded pdb=" O ILE B 601 " pdb=" O HOH B1001 " model vdw 2.223 3.040 nonbonded pdb=" O ILE A 601 " pdb=" O HOH A1001 " model vdw 2.227 3.040 nonbonded pdb=" O MET A 648 " pdb=" OG1 THR A 651 " model vdw 2.244 3.040 ... (remaining 66876 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 378 through 876 or resid 903 or resid 905 through 907)) selection = (chain 'B' and (resid 378 through 876 or resid 903 or resid 905 through 907)) } 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=0.00 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: 3.120 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.370 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.004 0.062 7846 Z= 0.248 Angle : 0.647 5.608 10574 Z= 0.392 Chirality : 0.040 0.164 1262 Planarity : 0.005 0.044 1226 Dihedral : 19.662 86.987 2956 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.41 % Allowed : 24.94 % Favored : 72.66 % 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: 0.34 (0.27), residues: 962 helix: 0.71 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.99 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 639 HIS 0.004 0.001 HIS B 439 PHE 0.030 0.002 PHE B 643 TYR 0.013 0.001 TYR B 841 ARG 0.001 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.815 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 1.2116 time to fit residues: 135.2659 Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.144932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118720 restraints weight = 7755.631| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.46 r_work: 0.3298 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7846 Z= 0.308 Angle : 0.606 5.834 10574 Z= 0.310 Chirality : 0.042 0.139 1262 Planarity : 0.005 0.044 1226 Dihedral : 16.686 84.704 1377 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.68 % Allowed : 22.41 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 962 helix: 0.99 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.86 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.005 0.002 HIS B 439 PHE 0.031 0.002 PHE B 643 TYR 0.012 0.002 TYR B 841 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.795 Fit side-chains REVERT: A 431 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.5997 (tptt) REVERT: B 537 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7018 (ptp-170) REVERT: B 735 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7166 (tttm) REVERT: B 801 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6537 (mttt) REVERT: B 850 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7192 (mpt180) outliers start: 37 outliers final: 14 residues processed: 113 average time/residue: 1.4000 time to fit residues: 167.6477 Evaluate side-chains 108 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.146817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121480 restraints weight = 7976.542| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.40 r_work: 0.3348 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7846 Z= 0.212 Angle : 0.537 5.378 10574 Z= 0.274 Chirality : 0.039 0.133 1262 Planarity : 0.005 0.042 1226 Dihedral : 16.172 80.650 1368 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.18 % Allowed : 21.65 % Favored : 74.18 % 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: 1.32 (0.27), residues: 962 helix: 1.44 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.004 0.001 HIS B 439 PHE 0.027 0.002 PHE B 643 TYR 0.010 0.001 TYR B 841 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.824 Fit side-chains REVERT: A 431 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.5979 (tptt) REVERT: B 407 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7054 (mtmm) REVERT: B 537 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6959 (ptp-170) REVERT: B 801 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6466 (mttt) REVERT: B 850 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7158 (mpt180) outliers start: 33 outliers final: 14 residues processed: 106 average time/residue: 1.3128 time to fit residues: 147.3759 Evaluate side-chains 103 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 407 LYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 0.0770 chunk 39 optimal weight: 0.2980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.150958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125551 restraints weight = 7725.635| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.44 r_work: 0.3392 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7846 Z= 0.143 Angle : 0.486 5.268 10574 Z= 0.245 Chirality : 0.038 0.129 1262 Planarity : 0.004 0.037 1226 Dihedral : 15.231 78.934 1366 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.91 % Allowed : 22.41 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.27), residues: 962 helix: 1.88 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.59 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 553 HIS 0.003 0.001 HIS B 439 PHE 0.023 0.001 PHE B 643 TYR 0.007 0.001 TYR B 841 ARG 0.001 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.851 Fit side-chains REVERT: A 431 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.5954 (tptt) REVERT: B 801 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6402 (mttt) outliers start: 23 outliers final: 4 residues processed: 99 average time/residue: 1.2345 time to fit residues: 129.9638 Evaluate side-chains 91 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.142963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117242 restraints weight = 7841.421| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.42 r_work: 0.3290 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7846 Z= 0.445 Angle : 0.672 7.301 10574 Z= 0.339 Chirality : 0.047 0.157 1262 Planarity : 0.005 0.044 1226 Dihedral : 15.754 83.718 1358 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.18 % Allowed : 21.90 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 962 helix: 1.27 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 553 HIS 0.005 0.002 HIS B 439 PHE 0.035 0.003 PHE A 643 TYR 0.012 0.002 TYR B 841 ARG 0.004 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.923 Fit side-chains REVERT: A 651 THR cc_start: 0.6478 (m) cc_final: 0.6228 (m) REVERT: A 875 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7244 (mmmt) REVERT: B 497 MET cc_start: 0.8780 (mmm) cc_final: 0.8408 (mtt) REVERT: B 537 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6922 (ptp-170) REVERT: B 611 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7518 (p) REVERT: B 801 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6574 (mttt) REVERT: B 850 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6612 (mpt-90) REVERT: B 875 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7198 (mmmt) outliers start: 33 outliers final: 15 residues processed: 98 average time/residue: 1.2577 time to fit residues: 131.2572 Evaluate side-chains 94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.148466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123017 restraints weight = 7678.190| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.42 r_work: 0.3346 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7846 Z= 0.179 Angle : 0.510 5.309 10574 Z= 0.258 Chirality : 0.039 0.127 1262 Planarity : 0.004 0.038 1226 Dihedral : 14.899 87.626 1358 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.41 % Allowed : 23.92 % Favored : 73.67 % 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: 1.80 (0.27), residues: 962 helix: 1.80 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.60 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.024 0.001 PHE B 643 TYR 0.008 0.001 TYR B 841 ARG 0.001 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.886 Fit side-chains REVERT: A 431 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.5977 (tptt) REVERT: A 651 THR cc_start: 0.6245 (m) cc_final: 0.5997 (m) REVERT: B 611 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7563 (p) REVERT: B 801 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6385 (mttt) outliers start: 19 outliers final: 7 residues processed: 92 average time/residue: 1.3052 time to fit residues: 127.8044 Evaluate side-chains 89 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0970 chunk 7 optimal weight: 0.0020 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.148235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121870 restraints weight = 7812.582| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.48 r_work: 0.3366 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7846 Z= 0.159 Angle : 0.498 5.274 10574 Z= 0.249 Chirality : 0.038 0.131 1262 Planarity : 0.004 0.037 1226 Dihedral : 14.078 89.157 1358 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.66 % Allowed : 23.29 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.27), residues: 962 helix: 2.00 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.53 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.023 0.001 PHE B 643 TYR 0.008 0.001 TYR B 518 ARG 0.001 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.816 Fit side-chains REVERT: A 651 THR cc_start: 0.6225 (m) cc_final: 0.5983 (m) REVERT: B 611 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7709 (p) REVERT: B 850 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.5948 (mpt-90) outliers start: 21 outliers final: 8 residues processed: 94 average time/residue: 1.2568 time to fit residues: 125.9570 Evaluate side-chains 91 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 850 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.148121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122449 restraints weight = 7769.473| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.42 r_work: 0.3349 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7846 Z= 0.215 Angle : 0.531 5.384 10574 Z= 0.267 Chirality : 0.040 0.134 1262 Planarity : 0.004 0.038 1226 Dihedral : 13.986 87.127 1354 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.03 % Allowed : 24.56 % Favored : 73.42 % 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: 1.93 (0.27), residues: 962 helix: 1.88 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.54 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 553 HIS 0.003 0.002 HIS B 439 PHE 0.027 0.002 PHE B 643 TYR 0.009 0.001 TYR A 841 ARG 0.006 0.001 ARG B 836 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.823 Fit side-chains REVERT: A 431 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.5990 (tptt) REVERT: A 651 THR cc_start: 0.6237 (m) cc_final: 0.5981 (m) REVERT: A 875 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7470 (mmmt) REVERT: B 611 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7635 (p) REVERT: B 850 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.6021 (mpt-90) outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 1.3162 time to fit residues: 122.7044 Evaluate side-chains 92 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 850 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.145950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121123 restraints weight = 7892.500| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.38 r_work: 0.3343 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7846 Z= 0.223 Angle : 0.539 5.399 10574 Z= 0.271 Chirality : 0.040 0.140 1262 Planarity : 0.004 0.038 1226 Dihedral : 14.001 84.855 1354 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.66 % Allowed : 24.43 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.27), residues: 962 helix: 1.84 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.54 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 553 HIS 0.004 0.002 HIS B 439 PHE 0.027 0.002 PHE B 643 TYR 0.009 0.001 TYR A 841 ARG 0.007 0.001 ARG B 836 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.799 Fit side-chains REVERT: A 431 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6000 (tptt) REVERT: A 651 THR cc_start: 0.6250 (m) cc_final: 0.5962 (m) REVERT: A 801 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6387 (mttm) REVERT: B 611 SER cc_start: 0.7915 (OUTLIER) cc_final: 0.7632 (p) REVERT: B 850 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.6092 (mpt-90) outliers start: 21 outliers final: 11 residues processed: 91 average time/residue: 1.3149 time to fit residues: 126.7139 Evaluate side-chains 92 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.145662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119856 restraints weight = 7803.286| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.42 r_work: 0.3318 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7846 Z= 0.311 Angle : 0.591 5.999 10574 Z= 0.298 Chirality : 0.043 0.144 1262 Planarity : 0.005 0.040 1226 Dihedral : 14.425 83.725 1354 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.77 % Allowed : 25.44 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 962 helix: 1.61 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.55 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.004 0.002 HIS B 439 PHE 0.031 0.002 PHE B 643 TYR 0.010 0.001 TYR A 841 ARG 0.007 0.001 ARG B 836 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.780 Fit side-chains REVERT: A 431 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.5991 (tptt) REVERT: A 651 THR cc_start: 0.6263 (m) cc_final: 0.5975 (m) REVERT: B 611 SER cc_start: 0.7837 (OUTLIER) cc_final: 0.7563 (p) REVERT: B 850 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.6285 (mpt-90) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 1.2986 time to fit residues: 118.2597 Evaluate side-chains 90 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.146543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121766 restraints weight = 7779.229| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.37 r_work: 0.3348 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7846 Z= 0.195 Angle : 0.528 5.357 10574 Z= 0.265 Chirality : 0.040 0.132 1262 Planarity : 0.004 0.039 1226 Dihedral : 14.023 84.291 1354 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.90 % Allowed : 25.70 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.27), residues: 962 helix: 1.81 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.56 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 639 HIS 0.003 0.002 HIS B 439 PHE 0.026 0.001 PHE B 643 TYR 0.008 0.001 TYR B 841 ARG 0.007 0.001 ARG B 836 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5083.33 seconds wall clock time: 91 minutes 36.52 seconds (5496.52 seconds total)