Starting phenix.real_space_refine on Thu Jul 2 09:16:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r33_18859/07_2026/8r33_18859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r33_18859/07_2026/8r33_18859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r33_18859/07_2026/8r33_18859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r33_18859/07_2026/8r33_18859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r33_18859/07_2026/8r33_18859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r33_18859/07_2026/8r33_18859.map" } resolution = 2.29 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= 0.000 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 52 5.16 5 C 5202 2.51 5 N 1148 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8066 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3677 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3677 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'3PH': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'3PH': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 166 Classifications: {'water': 166} Link IDs: {None: 165} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Time building chain proxies: 1.76, per 1000 atoms: 0.22 Number of scatterers: 8066 At special positions: 0 Unit cell: (108.297, 100.275, 74.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 8 15.00 O 1656 8.00 N 1148 7.00 C 5202 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: 0.53 Conformation dependent library (CDL) restraints added in 288.1 milliseconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 79.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 411 through 430 Processing helix chain 'A' and resid 435 through 455 Processing helix chain 'A' and resid 458 through 474 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.831A pdb=" N MET A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TRP A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 Processing helix chain 'A' and resid 519 through 533 removed outlier: 4.001A pdb=" N VAL A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 555 removed outlier: 3.676A 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 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 707 removed outlier: 3.973A pdb=" N ILE A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) Proline residue: A 701 - end of helix Processing helix chain 'A' and resid 712 through 718 Processing helix chain 'A' and resid 720 through 741 removed outlier: 3.803A pdb=" N VAL A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 removed outlier: 3.515A pdb=" N LYS A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.778A pdb=" N PHE A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 797 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 801 through 814 Processing helix chain 'A' and resid 824 through 833 Processing helix chain 'A' and resid 843 through 874 Proline residue: A 853 - end of helix removed outlier: 4.741A pdb=" N TYR A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 435 through 455 removed outlier: 3.535A pdb=" N ALA B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 474 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 485 through 496 Processing helix chain 'B' and resid 499 through 518 Processing helix chain 'B' and resid 520 through 533 removed outlier: 3.666A pdb=" N TRP B 527 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 555 removed outlier: 3.748A 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 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 Processing helix chain 'B' and resid 698 through 707 removed outlier: 3.813A 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: 3.836A pdb=" N VAL B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 removed outlier: 3.724A pdb=" N LYS B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 777 removed outlier: 3.706A pdb=" N PHE B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 797 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 801 through 814 Processing helix chain 'B' and resid 824 through 831 Processing helix chain 'B' and resid 843 through 874 Proline residue: B 853 - end of helix removed outlier: 4.730A pdb=" N TYR B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 872 " --> pdb=" O GLY B 868 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 384 through 387 removed outlier: 3.534A pdb=" N TRP A 387 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 403 " --> pdb=" O TRP A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 384 through 387 removed outlier: 3.509A pdb=" N VAL B 403 " --> pdb=" O TRP B 387 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1593 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: 1.15 Time building geometry restraints manager: 0.69 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: 1197 1.33 - 1.45: 1895 1.45 - 1.57: 4704 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7890 Sorted by residual: bond pdb=" N VAL A 403 " pdb=" CA VAL A 403 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.22e-02 6.72e+03 1.35e+00 bond pdb=" N VAL B 403 " pdb=" CA VAL B 403 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.22e-02 6.72e+03 1.34e+00 bond pdb=" CB GLU B 513 " pdb=" CG GLU B 513 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.04e-01 bond pdb=" CB GLU A 513 " pdb=" CG GLU A 513 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.09e-01 bond pdb=" CA PHE A 643 " pdb=" CB PHE A 643 " ideal model delta sigma weight residual 1.531 1.546 -0.015 1.72e-02 3.38e+03 7.69e-01 ... (remaining 7885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 10159 1.12 - 2.25: 372 2.25 - 3.37: 60 3.37 - 4.49: 24 4.49 - 5.62: 19 Bond angle restraints: 10634 Sorted by residual: angle pdb=" C ILE B 699 " pdb=" N ILE B 700 " pdb=" CA ILE B 700 " ideal model delta sigma weight residual 120.33 122.74 -2.41 8.00e-01 1.56e+00 9.11e+00 angle pdb=" C ILE A 699 " pdb=" N ILE A 700 " pdb=" CA ILE A 700 " ideal model delta sigma weight residual 120.33 122.73 -2.40 8.00e-01 1.56e+00 9.01e+00 angle pdb=" C LEU A 642 " pdb=" N PHE A 643 " pdb=" CA PHE A 643 " ideal model delta sigma weight residual 121.94 116.95 4.99 2.00e+00 2.50e-01 6.23e+00 angle pdb=" CB GLU A 513 " pdb=" CG GLU A 513 " pdb=" CD GLU A 513 " ideal model delta sigma weight residual 112.60 116.75 -4.15 1.70e+00 3.46e-01 5.96e+00 angle pdb=" C VAL A 466 " pdb=" CA VAL A 466 " pdb=" CB VAL A 466 " ideal model delta sigma weight residual 114.00 110.83 3.17 1.31e+00 5.83e-01 5.85e+00 ... (remaining 10629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3986 17.65 - 35.31: 505 35.31 - 52.96: 186 52.96 - 70.61: 29 70.61 - 88.26: 2 Dihedral angle restraints: 4708 sinusoidal: 1902 harmonic: 2806 Sorted by residual: dihedral pdb=" CA ILE A 785 " pdb=" C ILE A 785 " pdb=" N ILE A 786 " pdb=" CA ILE A 786 " ideal model delta harmonic sigma weight residual -180.00 -163.81 -16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU B 688 " pdb=" CG GLU B 688 " pdb=" CD GLU B 688 " pdb=" OE1 GLU B 688 " ideal model delta sinusoidal sigma weight residual 0.00 -88.26 88.26 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA GLU A 654 " pdb=" CB GLU A 654 " pdb=" CG GLU A 654 " pdb=" CD GLU A 654 " ideal model delta sinusoidal sigma weight residual -60.00 -119.59 59.59 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 780 0.028 - 0.055: 321 0.055 - 0.083: 112 0.083 - 0.111: 51 0.111 - 0.138: 6 Chirality restraints: 1270 Sorted by residual: chirality pdb=" CA PHE A 643 " pdb=" N PHE A 643 " pdb=" C PHE A 643 " pdb=" CB PHE A 643 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE B 457 " pdb=" N ILE B 457 " pdb=" C ILE B 457 " pdb=" CB ILE B 457 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA PHE B 643 " pdb=" N PHE B 643 " pdb=" C PHE B 643 " pdb=" CB PHE B 643 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1267 not shown) Planarity restraints: 1238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 457 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 458 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 862 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C VAL A 862 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL A 862 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 863 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 568 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 569 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 569 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 569 " 0.020 5.00e-02 4.00e+02 ... (remaining 1235 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 383 2.72 - 3.26: 8307 3.26 - 3.81: 14416 3.81 - 4.35: 18964 4.35 - 4.90: 29769 Nonbonded interactions: 71839 Sorted by model distance: nonbonded pdb=" OD1 ASN B 606 " pdb=" O HOH B1001 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASN A 606 " pdb=" O HOH A1001 " model vdw 2.185 3.040 nonbonded pdb=" O TRP B 498 " pdb=" O HOH B1002 " model vdw 2.194 3.040 nonbonded pdb=" O SER A 565 " pdb=" OG SER A 568 " model vdw 2.204 3.040 nonbonded pdb=" O TRP A 498 " pdb=" O HOH A1002 " model vdw 2.204 3.040 ... (remaining 71834 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 12.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.820 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 : 0.003 0.031 7890 Z= 0.133 Angle : 0.557 5.617 10634 Z= 0.307 Chirality : 0.037 0.138 1270 Planarity : 0.004 0.047 1238 Dihedral : 17.602 88.262 2900 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.39 % Allowed : 20.53 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.26), residues: 970 helix: 1.52 (0.19), residues: 714 sheet: -0.33 (1.04), residues: 24 loop : -0.31 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 836 TYR 0.013 0.002 TYR A 518 PHE 0.021 0.001 PHE A 643 TRP 0.006 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 7890) covalent geometry : angle 0.55665 / 0.31 (10634) hydrogen bonds : bond 0.18053 / 12.18 ( 531) hydrogen bonds : angle 7.03763 / 5.05 ( 1593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.272 Fit side-chains REVERT: B 531 PHE cc_start: 0.7542 (t80) cc_final: 0.6387 (m-10) REVERT: B 566 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7992 (tp) outliers start: 19 outliers final: 14 residues processed: 107 average time/residue: 0.5140 time to fit residues: 58.3041 Evaluate side-chains 104 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 ASN B 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105315 restraints weight = 7857.290| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.24 r_work: 0.3146 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7890 Z= 0.184 Angle : 0.604 6.073 10634 Z= 0.317 Chirality : 0.041 0.148 1270 Planarity : 0.005 0.044 1238 Dihedral : 13.357 58.380 1317 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.02 % Allowed : 18.64 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.27), residues: 970 helix: 1.83 (0.19), residues: 728 sheet: -0.15 (1.03), residues: 24 loop : -0.02 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 836 TYR 0.018 0.002 TYR A 518 PHE 0.024 0.002 PHE B 643 TRP 0.011 0.001 TRP A 721 HIS 0.009 0.002 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 7890) covalent geometry : angle 0.60424 / 0.32 (10634) hydrogen bonds : bond 0.05625 / 3.72 ( 531) hydrogen bonds : angle 5.17419 / 3.72 ( 1593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.206 Fit side-chains REVERT: A 657 LYS cc_start: 0.7359 (mmpt) cc_final: 0.7149 (mmtm) REVERT: B 566 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7865 (tp) REVERT: B 647 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7347 (mppt) outliers start: 24 outliers final: 8 residues processed: 108 average time/residue: 0.5467 time to fit residues: 62.6198 Evaluate side-chains 98 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 606 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 = 0.3642 r_free = 0.3642 target = 0.135560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108973 restraints weight = 7909.896| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.27 r_work: 0.3202 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7890 Z= 0.132 Angle : 0.528 5.154 10634 Z= 0.274 Chirality : 0.038 0.145 1270 Planarity : 0.004 0.042 1238 Dihedral : 12.622 58.513 1304 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.27 % Allowed : 18.14 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.38 (0.27), residues: 970 helix: 2.12 (0.19), residues: 724 sheet: 0.04 (1.05), residues: 24 loop : -0.03 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 836 TYR 0.015 0.001 TYR A 518 PHE 0.025 0.001 PHE B 643 TRP 0.008 0.001 TRP A 721 HIS 0.005 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7890) covalent geometry : angle 0.52755 / 0.27 (10634) hydrogen bonds : bond 0.04587 / 3.02 ( 531) hydrogen bonds : angle 4.78328 / 3.44 ( 1593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.298 Fit side-chains REVERT: A 497 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8117 (mtm) REVERT: A 651 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7760 (p) REVERT: A 657 LYS cc_start: 0.7318 (mmpt) cc_final: 0.7096 (mmtm) REVERT: B 770 MET cc_start: 0.8165 (mtp) cc_final: 0.7963 (mtp) outliers start: 18 outliers final: 6 residues processed: 103 average time/residue: 0.5682 time to fit residues: 61.9720 Evaluate side-chains 96 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 chunk 29 optimal weight: 0.9980 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106467 restraints weight = 8042.341| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.27 r_work: 0.3167 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7890 Z= 0.165 Angle : 0.570 5.981 10634 Z= 0.296 Chirality : 0.040 0.149 1270 Planarity : 0.004 0.042 1238 Dihedral : 12.656 59.702 1296 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.14 % Allowed : 17.76 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.27 (0.27), residues: 970 helix: 1.99 (0.19), residues: 728 sheet: -0.03 (1.02), residues: 24 loop : 0.12 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 836 TYR 0.019 0.001 TYR A 518 PHE 0.025 0.002 PHE B 643 TRP 0.010 0.001 TRP A 721 HIS 0.009 0.002 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 7890) covalent geometry : angle 0.56960 / 0.30 (10634) hydrogen bonds : bond 0.05117 / 3.39 ( 531) hydrogen bonds : angle 4.89313 / 3.52 ( 1593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.276 Fit side-chains REVERT: A 770 MET cc_start: 0.8164 (mtp) cc_final: 0.7762 (mtm) REVERT: B 647 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7397 (mppt) REVERT: B 770 MET cc_start: 0.8214 (mtp) cc_final: 0.7945 (mtp) outliers start: 17 outliers final: 8 residues processed: 102 average time/residue: 0.5124 time to fit residues: 55.4091 Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.103334 restraints weight = 7973.203| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.27 r_work: 0.3123 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7890 Z= 0.272 Angle : 0.702 8.600 10634 Z= 0.364 Chirality : 0.047 0.165 1270 Planarity : 0.005 0.043 1238 Dihedral : 13.604 59.921 1296 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.64 % Allowed : 18.01 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.26), residues: 970 helix: 1.71 (0.19), residues: 720 sheet: -0.34 (0.97), residues: 24 loop : -0.17 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 440 TYR 0.024 0.002 TYR A 518 PHE 0.024 0.002 PHE B 643 TRP 0.016 0.002 TRP A 721 HIS 0.012 0.002 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.27 ( 7890) covalent geometry : angle 0.70170 / 0.36 (10634) hydrogen bonds : bond 0.06253 / 4.17 ( 531) hydrogen bonds : angle 5.25880 / 3.79 ( 1593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.331 Fit side-chains REVERT: A 657 LYS cc_start: 0.7306 (mmpt) cc_final: 0.7030 (mmtm) REVERT: A 688 GLU cc_start: 0.8100 (tt0) cc_final: 0.7817 (tt0) REVERT: B 647 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7410 (mppt) REVERT: B 657 LYS cc_start: 0.7292 (mmpt) cc_final: 0.7076 (mmtm) REVERT: B 770 MET cc_start: 0.8285 (mtp) cc_final: 0.8058 (mtp) outliers start: 21 outliers final: 11 residues processed: 104 average time/residue: 0.5289 time to fit residues: 58.4298 Evaluate side-chains 100 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 chunk 78 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109244 restraints weight = 7931.023| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.26 r_work: 0.3206 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7890 Z= 0.123 Angle : 0.526 6.044 10634 Z= 0.271 Chirality : 0.038 0.140 1270 Planarity : 0.004 0.041 1238 Dihedral : 12.543 59.776 1296 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.14 % Allowed : 18.26 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.27), residues: 970 helix: 2.14 (0.19), residues: 726 sheet: -0.08 (1.05), residues: 24 loop : 0.14 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 840 TYR 0.013 0.001 TYR A 518 PHE 0.023 0.001 PHE B 643 TRP 0.008 0.001 TRP A 721 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7890) covalent geometry : angle 0.52638 / 0.27 (10634) hydrogen bonds : bond 0.04223 / 2.78 ( 531) hydrogen bonds : angle 4.67089 / 3.36 ( 1593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.286 Fit side-chains REVERT: A 651 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7779 (p) REVERT: A 657 LYS cc_start: 0.7257 (mmpt) cc_final: 0.6974 (mmtm) REVERT: A 770 MET cc_start: 0.8125 (mtp) cc_final: 0.7734 (mtm) REVERT: A 845 MET cc_start: 0.8477 (tpp) cc_final: 0.8216 (tpp) REVERT: B 647 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7383 (mppt) REVERT: B 651 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7815 (p) REVERT: B 657 LYS cc_start: 0.7257 (mmpt) cc_final: 0.6973 (mmtm) REVERT: B 845 MET cc_start: 0.8479 (tpp) cc_final: 0.8216 (tpp) outliers start: 17 outliers final: 5 residues processed: 102 average time/residue: 0.5185 time to fit residues: 56.1340 Evaluate side-chains 95 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106214 restraints weight = 7969.977| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.27 r_work: 0.3166 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7890 Z= 0.170 Angle : 0.582 6.108 10634 Z= 0.301 Chirality : 0.040 0.152 1270 Planarity : 0.004 0.042 1238 Dihedral : 12.644 59.852 1296 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.14 % Allowed : 18.39 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.27 (0.27), residues: 970 helix: 2.02 (0.19), residues: 726 sheet: -0.12 (1.03), residues: 24 loop : 0.05 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 840 TYR 0.020 0.002 TYR A 518 PHE 0.025 0.002 PHE B 643 TRP 0.010 0.001 TRP A 721 HIS 0.009 0.002 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 7890) covalent geometry : angle 0.58168 / 0.30 (10634) hydrogen bonds : bond 0.05044 / 3.35 ( 531) hydrogen bonds : angle 4.86164 / 3.50 ( 1593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.189 Fit side-chains REVERT: A 402 ASN cc_start: 0.5532 (OUTLIER) cc_final: 0.5248 (p0) REVERT: A 651 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7801 (p) REVERT: A 657 LYS cc_start: 0.7253 (mmpt) cc_final: 0.6955 (mmtm) REVERT: A 770 MET cc_start: 0.8175 (mtp) cc_final: 0.7753 (mtm) REVERT: B 647 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7391 (mppt) REVERT: B 651 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7833 (p) REVERT: B 657 LYS cc_start: 0.7285 (mmpt) cc_final: 0.7038 (mmtm) REVERT: B 753 LYS cc_start: 0.7347 (pttt) cc_final: 0.7062 (ptmm) outliers start: 17 outliers final: 9 residues processed: 103 average time/residue: 0.4821 time to fit residues: 52.7742 Evaluate side-chains 101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104365 restraints weight = 7924.079| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.27 r_work: 0.3137 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7890 Z= 0.224 Angle : 0.649 7.619 10634 Z= 0.336 Chirality : 0.044 0.160 1270 Planarity : 0.004 0.043 1238 Dihedral : 13.037 59.869 1296 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.52 % Allowed : 18.14 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.27), residues: 970 helix: 1.82 (0.19), residues: 724 sheet: -0.13 (1.01), residues: 24 loop : -0.08 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 840 TYR 0.023 0.002 TYR A 518 PHE 0.025 0.002 PHE B 643 TRP 0.013 0.002 TRP A 721 HIS 0.011 0.002 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 ( 7890) covalent geometry : angle 0.64929 / 0.34 (10634) hydrogen bonds : bond 0.05716 / 3.81 ( 531) hydrogen bonds : angle 5.06844 / 3.65 ( 1593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.203 Fit side-chains REVERT: A 647 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7351 (mppt) REVERT: A 651 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7848 (p) REVERT: A 770 MET cc_start: 0.8236 (mtp) cc_final: 0.7806 (mtm) REVERT: A 840 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.8071 (mmm-85) REVERT: B 647 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7395 (mppt) REVERT: B 657 LYS cc_start: 0.7289 (mmpt) cc_final: 0.7022 (mmtm) REVERT: B 753 LYS cc_start: 0.7332 (pttt) cc_final: 0.6996 (ptmm) REVERT: B 770 MET cc_start: 0.8232 (mtp) cc_final: 0.7791 (mtm) REVERT: B 840 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.8089 (mmm-85) outliers start: 20 outliers final: 9 residues processed: 107 average time/residue: 0.4903 time to fit residues: 55.5389 Evaluate side-chains 98 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107781 restraints weight = 7926.892| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.26 r_work: 0.3187 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7890 Z= 0.137 Angle : 0.545 5.400 10634 Z= 0.283 Chirality : 0.039 0.142 1270 Planarity : 0.004 0.042 1238 Dihedral : 12.365 59.795 1296 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.51 % Allowed : 19.52 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.37 (0.27), residues: 970 helix: 2.08 (0.19), residues: 726 sheet: 0.06 (1.03), residues: 24 loop : 0.10 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 850 TYR 0.016 0.001 TYR A 518 PHE 0.024 0.001 PHE B 643 TRP 0.009 0.001 TRP A 721 HIS 0.005 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 7890) covalent geometry : angle 0.54513 / 0.28 (10634) hydrogen bonds : bond 0.04531 / 3.00 ( 531) hydrogen bonds : angle 4.72974 / 3.40 ( 1593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.194 Fit side-chains REVERT: A 647 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7356 (mppt) REVERT: A 651 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7782 (p) REVERT: A 657 LYS cc_start: 0.7255 (mmpt) cc_final: 0.6976 (mmtm) REVERT: A 753 LYS cc_start: 0.7268 (pttt) cc_final: 0.6917 (ptmm) REVERT: A 770 MET cc_start: 0.8197 (mtp) cc_final: 0.7755 (mtm) REVERT: B 647 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7381 (mppt) REVERT: B 651 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7843 (p) REVERT: B 657 LYS cc_start: 0.7301 (mmpt) cc_final: 0.7014 (mmtm) REVERT: B 753 LYS cc_start: 0.7306 (pttt) cc_final: 0.6987 (ptmm) REVERT: B 770 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7766 (mtm) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 0.4975 time to fit residues: 51.5703 Evaluate side-chains 101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 786 ILE 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 39 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104801 restraints weight = 7909.198| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.26 r_work: 0.3144 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7890 Z= 0.213 Angle : 0.639 7.153 10634 Z= 0.331 Chirality : 0.043 0.158 1270 Planarity : 0.004 0.043 1238 Dihedral : 12.837 59.856 1296 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.76 % Allowed : 19.27 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.04 (0.27), residues: 970 helix: 1.87 (0.19), residues: 724 sheet: -0.14 (0.99), residues: 24 loop : -0.08 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 840 TYR 0.022 0.002 TYR A 518 PHE 0.025 0.002 PHE B 643 TRP 0.012 0.002 TRP A 721 HIS 0.010 0.002 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 ( 7890) covalent geometry : angle 0.63944 / 0.33 (10634) hydrogen bonds : bond 0.05585 / 3.72 ( 531) hydrogen bonds : angle 5.01398 / 3.61 ( 1593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.300 Fit side-chains REVERT: A 474 LYS cc_start: 0.8674 (mttm) cc_final: 0.8471 (mttm) REVERT: A 647 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7355 (mppt) REVERT: A 651 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7830 (p) REVERT: A 657 LYS cc_start: 0.7248 (mmpt) cc_final: 0.6944 (mmtm) REVERT: A 753 LYS cc_start: 0.7280 (pttt) cc_final: 0.6931 (ptmm) REVERT: B 647 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7388 (mppt) REVERT: B 651 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7872 (p) REVERT: B 657 LYS cc_start: 0.7317 (mmpt) cc_final: 0.7007 (mmtm) REVERT: B 753 LYS cc_start: 0.7346 (pttt) cc_final: 0.6990 (ptmm) REVERT: B 770 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7842 (mtm) outliers start: 14 outliers final: 8 residues processed: 101 average time/residue: 0.4969 time to fit residues: 53.1643 Evaluate side-chains 102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 786 ILE 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 31 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107800 restraints weight = 7874.068| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.25 r_work: 0.3187 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7890 Z= 0.137 Angle : 0.549 5.594 10634 Z= 0.284 Chirality : 0.039 0.143 1270 Planarity : 0.004 0.042 1238 Dihedral : 12.285 59.974 1296 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.64 % Allowed : 19.65 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.34 (0.27), residues: 970 helix: 2.07 (0.19), residues: 728 sheet: 0.12 (1.03), residues: 24 loop : 0.04 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 836 TYR 0.016 0.001 TYR A 518 PHE 0.024 0.001 PHE B 643 TRP 0.009 0.001 TRP A 721 HIS 0.005 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 7890) covalent geometry : angle 0.54873 / 0.28 (10634) hydrogen bonds : bond 0.04540 / 3.01 ( 531) hydrogen bonds : angle 4.72590 / 3.40 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2792.32 seconds wall clock time: 48 minutes 23.14 seconds (2903.14 seconds total)