Starting phenix.real_space_refine on Fri Aug 22 16:05:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k12_36784/08_2025/8k12_36784_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k12_36784/08_2025/8k12_36784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k12_36784/08_2025/8k12_36784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k12_36784/08_2025/8k12_36784.map" model { file = "/net/cci-nas-00/data/ceres_data/8k12_36784/08_2025/8k12_36784_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k12_36784/08_2025/8k12_36784_neut.cif" } resolution = 3.3 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= 0.046 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 3730 2.51 5 N 872 2.21 5 O 942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5592 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2796 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 349} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2796 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 349} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 1.59, per 1000 atoms: 0.28 Number of scatterers: 5592 At special positions: 0 Unit cell: (99.22, 71.34, 77.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 942 8.00 N 872 7.00 C 3730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 787 " distance=2.03 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: 0.47 Conformation dependent library (CDL) restraints added in 221.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1348 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 80.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 289 through 317 removed outlier: 3.991A pdb=" N TYR A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 479 removed outlier: 3.554A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.620A pdb=" N ILE A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.836A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 removed outlier: 3.709A pdb=" N GLY A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 596 removed outlier: 3.671A pdb=" N PHE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N MET A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 625 Processing helix chain 'A' and resid 630 through 652 removed outlier: 4.128A pdb=" N SER A 638 " --> pdb=" O TRP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 713 through 740 removed outlier: 3.562A pdb=" N LEU A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 734 " --> pdb=" O PHE A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 767 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 794 through 816 removed outlier: 3.666A pdb=" N ILE A 805 " --> pdb=" O PHE A 801 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 317 removed outlier: 3.996A pdb=" N TYR B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 479 removed outlier: 3.554A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix Processing helix chain 'B' and resid 499 through 505 removed outlier: 3.620A pdb=" N ILE B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.835A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 removed outlier: 3.709A pdb=" N GLY B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS B 568 " --> pdb=" O SER B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 596 removed outlier: 3.670A pdb=" N PHE B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N MET B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 625 Processing helix chain 'B' and resid 630 through 652 removed outlier: 4.128A pdb=" N SER B 638 " --> pdb=" O TRP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 Processing helix chain 'B' and resid 713 through 740 removed outlier: 3.562A pdb=" N LEU B 719 " --> pdb=" O ALA B 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 734 " --> pdb=" O PHE B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 767 removed outlier: 3.501A pdb=" N PHE B 761 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 794 through 816 removed outlier: 3.666A pdb=" N ILE B 805 " --> pdb=" O PHE B 801 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 814 " --> pdb=" O SER B 810 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1257 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: 0.93 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1678 1.35 - 1.46: 1456 1.46 - 1.58: 2522 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 5728 Sorted by residual: bond pdb=" N THR B 289 " pdb=" CA THR B 289 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.52e+00 bond pdb=" N THR A 289 " pdb=" CA THR A 289 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.32e+00 bond pdb=" N ILE B 586 " pdb=" CA ILE B 586 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.19e-02 7.06e+03 6.39e+00 bond pdb=" N ILE A 586 " pdb=" CA ILE A 586 " ideal model delta sigma weight residual 1.461 1.490 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N LEU B 592 " pdb=" CA LEU B 592 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.72e+00 ... (remaining 5723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7212 1.21 - 2.42: 430 2.42 - 3.64: 114 3.64 - 4.85: 30 4.85 - 6.06: 10 Bond angle restraints: 7796 Sorted by residual: angle pdb=" C SER A 295 " pdb=" N GLY A 296 " pdb=" CA GLY A 296 " ideal model delta sigma weight residual 119.98 124.36 -4.38 1.11e+00 8.12e-01 1.56e+01 angle pdb=" C SER B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta sigma weight residual 119.98 124.34 -4.36 1.11e+00 8.12e-01 1.55e+01 angle pdb=" C LEU A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta sigma weight residual 119.98 124.33 -4.35 1.11e+00 8.12e-01 1.54e+01 angle pdb=" C LEU B 301 " pdb=" N GLY B 302 " pdb=" CA GLY B 302 " ideal model delta sigma weight residual 119.98 124.21 -4.23 1.11e+00 8.12e-01 1.45e+01 angle pdb=" N GLN A 596 " pdb=" CA GLN A 596 " pdb=" C GLN A 596 " ideal model delta sigma weight residual 113.20 109.19 4.01 1.21e+00 6.83e-01 1.10e+01 ... (remaining 7791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 2875 16.04 - 32.07: 297 32.07 - 48.11: 80 48.11 - 64.15: 20 64.15 - 80.18: 4 Dihedral angle restraints: 3276 sinusoidal: 1196 harmonic: 2080 Sorted by residual: dihedral pdb=" CA PHE A 576 " pdb=" C PHE A 576 " pdb=" N GLN A 577 " pdb=" CA GLN A 577 " ideal model delta harmonic sigma weight residual -180.00 -151.93 -28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA PHE B 576 " pdb=" C PHE B 576 " pdb=" N GLN B 577 " pdb=" CA GLN B 577 " ideal model delta harmonic sigma weight residual 180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA MET B 559 " pdb=" C MET B 559 " pdb=" N GLU B 560 " pdb=" CA GLU B 560 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 3273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 660 0.042 - 0.085: 192 0.085 - 0.127: 43 0.127 - 0.169: 29 0.169 - 0.212: 10 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA ILE B 586 " pdb=" N ILE B 586 " pdb=" C ILE B 586 " pdb=" CB ILE B 586 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE A 586 " pdb=" N ILE A 586 " pdb=" C ILE A 586 " pdb=" CB ILE A 586 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR A 311 " pdb=" CA THR A 311 " pdb=" OG1 THR A 311 " pdb=" CG2 THR A 311 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 931 not shown) Planarity restraints: 942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 308 " 0.070 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR A 308 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 308 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 308 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 308 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 308 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 308 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 308 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 308 " -0.070 2.00e-02 2.50e+03 4.39e-02 3.85e+01 pdb=" CG TYR B 308 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 308 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 308 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR B 308 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR B 308 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 308 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 308 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 304 " 0.040 2.00e-02 2.50e+03 2.56e-02 1.14e+01 pdb=" CG PHE A 304 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 304 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 304 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 304 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 304 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 304 " 0.031 2.00e-02 2.50e+03 ... (remaining 939 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 580 2.75 - 3.29: 6039 3.29 - 3.82: 9252 3.82 - 4.36: 10919 4.36 - 4.90: 17906 Nonbonded interactions: 44696 Sorted by model distance: nonbonded pdb=" OH TYR A 293 " pdb=" O PRO A 493 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR A 486 " pdb=" O VAL A 569 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR B 486 " pdb=" O VAL B 569 " model vdw 2.228 3.040 nonbonded pdb=" O ASN B 501 " pdb=" OG SER B 505 " model vdw 2.262 3.040 nonbonded pdb=" O ASN A 501 " pdb=" OG SER A 505 " model vdw 2.263 3.040 ... (remaining 44691 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.005 0.036 5732 Z= 0.287 Angle : 0.711 6.061 7804 Z= 0.471 Chirality : 0.050 0.212 934 Planarity : 0.004 0.044 942 Dihedral : 14.817 80.183 1916 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.50 % Allowed : 16.22 % Favored : 83.28 % 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 aren not related in a simple way. whole: 1.25 (0.31), residues: 694 helix: 1.47 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.48 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 785 TYR 0.078 0.004 TYR A 308 PHE 0.040 0.002 PHE A 304 TRP 0.049 0.003 TRP A 317 HIS 0.002 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 5728) covalent geometry : angle 0.70959 ( 7796) SS BOND : bond 0.00163 ( 4) SS BOND : angle 1.62605 ( 8) hydrogen bonds : bond 0.23784 ( 419) hydrogen bonds : angle 7.37174 ( 1257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 286 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LEU cc_start: 0.7758 (mt) cc_final: 0.7504 (mt) REVERT: A 562 LEU cc_start: 0.6917 (tt) cc_final: 0.6691 (tt) REVERT: A 791 ASP cc_start: 0.7372 (m-30) cc_final: 0.7104 (t0) REVERT: A 794 ASP cc_start: 0.6138 (p0) cc_final: 0.5422 (p0) REVERT: A 797 ASP cc_start: 0.7077 (m-30) cc_final: 0.6830 (m-30) REVERT: B 308 TYR cc_start: 0.8073 (m-80) cc_final: 0.6944 (m-80) REVERT: B 462 LEU cc_start: 0.7815 (mt) cc_final: 0.7580 (mt) REVERT: B 562 LEU cc_start: 0.6933 (tt) cc_final: 0.6706 (tt) REVERT: B 791 ASP cc_start: 0.7429 (m-30) cc_final: 0.7045 (t0) REVERT: B 794 ASP cc_start: 0.6038 (p0) cc_final: 0.5311 (p0) REVERT: B 797 ASP cc_start: 0.7036 (m-30) cc_final: 0.6798 (m-30) outliers start: 3 outliers final: 0 residues processed: 286 average time/residue: 0.0662 time to fit residues: 25.7706 Evaluate side-chains 170 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN A 527 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS B 526 ASN B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.166192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.135733 restraints weight = 11729.318| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.53 r_work: 0.3884 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5732 Z= 0.171 Angle : 0.713 11.335 7804 Z= 0.360 Chirality : 0.043 0.149 934 Planarity : 0.004 0.022 942 Dihedral : 4.395 24.438 748 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.01 % Allowed : 23.58 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.30), residues: 694 helix: 1.85 (0.20), residues: 548 sheet: None (None), residues: 0 loop : -1.45 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 785 TYR 0.023 0.002 TYR B 717 PHE 0.044 0.003 PHE B 811 TRP 0.036 0.002 TRP B 700 HIS 0.008 0.001 HIS B 527 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5728) covalent geometry : angle 0.71287 ( 7796) SS BOND : bond 0.00053 ( 4) SS BOND : angle 1.16904 ( 8) hydrogen bonds : bond 0.05909 ( 419) hydrogen bonds : angle 4.49854 ( 1257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.8131 (m-80) cc_final: 0.7676 (m-80) REVERT: A 462 LEU cc_start: 0.8507 (mt) cc_final: 0.8298 (mt) REVERT: A 472 GLN cc_start: 0.8849 (tp40) cc_final: 0.8568 (tp40) REVERT: A 791 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7256 (t0) REVERT: B 462 LEU cc_start: 0.8508 (mt) cc_final: 0.8256 (mt) REVERT: B 472 GLN cc_start: 0.8907 (tp40) cc_final: 0.8674 (tp40) REVERT: B 709 MET cc_start: 0.7894 (tpp) cc_final: 0.7524 (tpp) REVERT: B 791 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7192 (t0) REVERT: B 811 PHE cc_start: 0.8830 (m-80) cc_final: 0.8601 (m-80) outliers start: 18 outliers final: 9 residues processed: 196 average time/residue: 0.0606 time to fit residues: 16.4471 Evaluate side-chains 175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.0000 chunk 6 optimal weight: 0.0970 chunk 58 optimal weight: 5.9990 chunk 31 optimal weight: 0.0060 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.166124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.135678 restraints weight = 11695.534| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.51 r_work: 0.3902 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5732 Z= 0.137 Angle : 0.608 9.097 7804 Z= 0.309 Chirality : 0.039 0.134 934 Planarity : 0.003 0.025 942 Dihedral : 4.329 24.531 748 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.01 % Allowed : 24.41 % Favored : 72.58 % 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 aren not related in a simple way. whole: 1.95 (0.30), residues: 694 helix: 2.00 (0.20), residues: 548 sheet: None (None), residues: 0 loop : -1.53 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 785 TYR 0.010 0.001 TYR A 486 PHE 0.024 0.002 PHE B 811 TRP 0.022 0.002 TRP B 700 HIS 0.009 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5728) covalent geometry : angle 0.60800 ( 7796) SS BOND : bond 0.00044 ( 4) SS BOND : angle 0.85346 ( 8) hydrogen bonds : bond 0.04902 ( 419) hydrogen bonds : angle 4.12824 ( 1257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.8145 (m-80) cc_final: 0.7719 (m-80) REVERT: A 462 LEU cc_start: 0.8480 (mt) cc_final: 0.8212 (mt) REVERT: A 472 GLN cc_start: 0.8848 (tp40) cc_final: 0.8464 (tp40) REVERT: A 585 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8214 (tmm) REVERT: A 736 MET cc_start: 0.8535 (mpp) cc_final: 0.8235 (ptp) REVERT: A 791 ASP cc_start: 0.8183 (m-30) cc_final: 0.7167 (t0) REVERT: B 462 LEU cc_start: 0.8450 (mt) cc_final: 0.8192 (mt) REVERT: B 472 GLN cc_start: 0.8866 (tp40) cc_final: 0.8570 (tp40) REVERT: B 700 TRP cc_start: 0.7908 (m-10) cc_final: 0.7502 (m-90) REVERT: B 709 MET cc_start: 0.7839 (tpp) cc_final: 0.7423 (tpp) REVERT: B 791 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7130 (t0) outliers start: 18 outliers final: 6 residues processed: 186 average time/residue: 0.0577 time to fit residues: 15.1635 Evaluate side-chains 169 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.164127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.133661 restraints weight = 12026.383| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 3.55 r_work: 0.3894 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5732 Z= 0.135 Angle : 0.636 13.044 7804 Z= 0.308 Chirality : 0.039 0.139 934 Planarity : 0.003 0.026 942 Dihedral : 4.271 24.012 748 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.85 % Allowed : 26.42 % Favored : 69.73 % 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 aren not related in a simple way. whole: 2.13 (0.30), residues: 694 helix: 2.15 (0.20), residues: 548 sheet: None (None), residues: 0 loop : -1.56 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 785 TYR 0.011 0.001 TYR A 573 PHE 0.020 0.002 PHE A 811 TRP 0.017 0.001 TRP B 700 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5728) covalent geometry : angle 0.63631 ( 7796) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.62534 ( 8) hydrogen bonds : bond 0.04593 ( 419) hydrogen bonds : angle 4.01898 ( 1257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LEU cc_start: 0.8462 (mt) cc_final: 0.8187 (mt) REVERT: A 472 GLN cc_start: 0.8817 (tp40) cc_final: 0.8441 (tp40) REVERT: A 585 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8200 (tmm) REVERT: A 791 ASP cc_start: 0.8214 (m-30) cc_final: 0.7223 (t0) REVERT: B 462 LEU cc_start: 0.8428 (mt) cc_final: 0.8221 (mt) REVERT: B 472 GLN cc_start: 0.8866 (tp40) cc_final: 0.8497 (tp40) REVERT: B 709 MET cc_start: 0.7840 (tpp) cc_final: 0.7379 (tpp) REVERT: B 791 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7143 (t0) outliers start: 23 outliers final: 11 residues processed: 176 average time/residue: 0.0571 time to fit residues: 14.3237 Evaluate side-chains 172 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 805 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.166114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.136594 restraints weight = 11969.151| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 3.45 r_work: 0.3966 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5732 Z= 0.130 Angle : 0.611 12.920 7804 Z= 0.299 Chirality : 0.039 0.151 934 Planarity : 0.003 0.025 942 Dihedral : 4.281 23.574 748 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.34 % Allowed : 26.92 % Favored : 69.73 % 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 aren not related in a simple way. whole: 2.14 (0.30), residues: 694 helix: 2.11 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -1.41 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 529 TYR 0.007 0.001 TYR B 486 PHE 0.026 0.002 PHE B 732 TRP 0.010 0.001 TRP A 700 HIS 0.013 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5728) covalent geometry : angle 0.61098 ( 7796) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.59856 ( 8) hydrogen bonds : bond 0.04382 ( 419) hydrogen bonds : angle 3.90687 ( 1257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LEU cc_start: 0.8404 (mt) cc_final: 0.8111 (mt) REVERT: A 472 GLN cc_start: 0.8584 (tp40) cc_final: 0.8340 (tp40) REVERT: A 585 MET cc_start: 0.8414 (tmm) cc_final: 0.8176 (tmm) REVERT: A 791 ASP cc_start: 0.8263 (m-30) cc_final: 0.7349 (t0) REVERT: B 450 PHE cc_start: 0.3236 (OUTLIER) cc_final: 0.2185 (t80) REVERT: B 462 LEU cc_start: 0.8411 (mt) cc_final: 0.8138 (mt) REVERT: B 472 GLN cc_start: 0.8637 (tp40) cc_final: 0.8401 (tp40) REVERT: B 583 MET cc_start: 0.8076 (ptp) cc_final: 0.7864 (ptm) REVERT: B 709 MET cc_start: 0.7891 (tpp) cc_final: 0.7423 (tpp) REVERT: B 775 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7832 (mmmt) REVERT: B 791 ASP cc_start: 0.8209 (m-30) cc_final: 0.7244 (t0) outliers start: 20 outliers final: 14 residues processed: 178 average time/residue: 0.0601 time to fit residues: 14.9264 Evaluate side-chains 168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 805 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.162451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.131981 restraints weight = 12082.776| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.54 r_work: 0.3861 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5732 Z= 0.148 Angle : 0.625 10.958 7804 Z= 0.307 Chirality : 0.038 0.158 934 Planarity : 0.003 0.025 942 Dihedral : 4.257 23.092 748 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.18 % Allowed : 26.76 % Favored : 69.06 % 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 aren not related in a simple way. whole: 2.29 (0.31), residues: 694 helix: 2.23 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -1.40 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 529 TYR 0.008 0.001 TYR B 485 PHE 0.031 0.002 PHE B 732 TRP 0.010 0.001 TRP B 799 HIS 0.010 0.001 HIS B 527 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5728) covalent geometry : angle 0.62505 ( 7796) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.59460 ( 8) hydrogen bonds : bond 0.04235 ( 419) hydrogen bonds : angle 3.93088 ( 1257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 PHE cc_start: 0.3463 (OUTLIER) cc_final: 0.2611 (t80) REVERT: A 462 LEU cc_start: 0.8397 (mt) cc_final: 0.8136 (mt) REVERT: A 472 GLN cc_start: 0.8771 (tp40) cc_final: 0.8399 (tp40) REVERT: A 585 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8273 (tmm) REVERT: A 791 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7343 (t0) REVERT: B 450 PHE cc_start: 0.3300 (OUTLIER) cc_final: 0.2392 (t80) REVERT: B 462 LEU cc_start: 0.8405 (mt) cc_final: 0.8161 (mt) REVERT: B 472 GLN cc_start: 0.8802 (tp40) cc_final: 0.8453 (tp40) REVERT: B 583 MET cc_start: 0.8389 (ptp) cc_final: 0.8137 (ptm) REVERT: B 709 MET cc_start: 0.7922 (tpp) cc_final: 0.7430 (tpp) REVERT: B 775 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7850 (mmmt) REVERT: B 791 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7272 (t0) outliers start: 25 outliers final: 17 residues processed: 170 average time/residue: 0.0594 time to fit residues: 14.2752 Evaluate side-chains 170 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.0970 chunk 63 optimal weight: 0.0040 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.163559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.133483 restraints weight = 12164.905| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.54 r_work: 0.3868 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5732 Z= 0.133 Angle : 0.654 12.483 7804 Z= 0.313 Chirality : 0.038 0.163 934 Planarity : 0.002 0.025 942 Dihedral : 4.289 22.614 748 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.85 % Allowed : 26.25 % Favored : 68.90 % 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 aren not related in a simple way. whole: 2.31 (0.31), residues: 694 helix: 2.23 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.23 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 781 TYR 0.007 0.001 TYR B 573 PHE 0.017 0.002 PHE A 811 TRP 0.014 0.001 TRP B 799 HIS 0.012 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5728) covalent geometry : angle 0.65439 ( 7796) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.54670 ( 8) hydrogen bonds : bond 0.04107 ( 419) hydrogen bonds : angle 4.03135 ( 1257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 PHE cc_start: 0.3552 (OUTLIER) cc_final: 0.2679 (t80) REVERT: A 472 GLN cc_start: 0.8786 (tp40) cc_final: 0.8375 (tp40) REVERT: A 585 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8263 (tmm) REVERT: A 791 ASP cc_start: 0.8295 (m-30) cc_final: 0.7329 (t0) REVERT: B 450 PHE cc_start: 0.3611 (OUTLIER) cc_final: 0.2667 (t80) REVERT: B 472 GLN cc_start: 0.8817 (tp40) cc_final: 0.8446 (tp40) REVERT: B 585 MET cc_start: 0.8097 (ptt) cc_final: 0.7836 (ptp) REVERT: B 709 MET cc_start: 0.7908 (tpp) cc_final: 0.7407 (tpp) REVERT: B 775 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7853 (mmmt) REVERT: B 791 ASP cc_start: 0.8294 (m-30) cc_final: 0.7260 (t0) outliers start: 29 outliers final: 12 residues processed: 174 average time/residue: 0.0560 time to fit residues: 13.8573 Evaluate side-chains 165 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.163323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.133422 restraints weight = 11948.817| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.49 r_work: 0.3924 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5732 Z= 0.146 Angle : 0.708 11.664 7804 Z= 0.340 Chirality : 0.040 0.175 934 Planarity : 0.003 0.025 942 Dihedral : 4.371 22.139 748 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.35 % Allowed : 27.59 % Favored : 68.06 % 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 aren not related in a simple way. whole: 2.20 (0.31), residues: 694 helix: 2.17 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.27 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 781 TYR 0.011 0.001 TYR B 308 PHE 0.048 0.002 PHE A 618 TRP 0.018 0.001 TRP B 799 HIS 0.012 0.001 HIS B 527 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5728) covalent geometry : angle 0.70786 ( 7796) SS BOND : bond 0.00097 ( 4) SS BOND : angle 0.54044 ( 8) hydrogen bonds : bond 0.04129 ( 419) hydrogen bonds : angle 4.14908 ( 1257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 PHE cc_start: 0.3656 (OUTLIER) cc_final: 0.2783 (t80) REVERT: A 472 GLN cc_start: 0.8779 (tp40) cc_final: 0.8366 (tp40) REVERT: A 710 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6571 (mtp-110) REVERT: A 764 PHE cc_start: 0.8216 (t80) cc_final: 0.7872 (t80) REVERT: A 791 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7329 (t0) REVERT: B 450 PHE cc_start: 0.3615 (OUTLIER) cc_final: 0.2696 (t80) REVERT: B 472 GLN cc_start: 0.8820 (tp40) cc_final: 0.8437 (tp40) REVERT: B 573 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6772 (m-10) REVERT: B 585 MET cc_start: 0.8117 (ptt) cc_final: 0.7854 (ptp) REVERT: B 709 MET cc_start: 0.7951 (tpp) cc_final: 0.7484 (tpp) REVERT: B 775 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7940 (mmmt) REVERT: B 791 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7265 (t0) outliers start: 26 outliers final: 16 residues processed: 167 average time/residue: 0.0578 time to fit residues: 13.6384 Evaluate side-chains 170 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 TRP Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 573 TYR Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.160781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.130599 restraints weight = 12076.431| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.47 r_work: 0.3852 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5732 Z= 0.187 Angle : 0.709 10.802 7804 Z= 0.351 Chirality : 0.042 0.191 934 Planarity : 0.003 0.025 942 Dihedral : 4.513 22.203 748 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.52 % Allowed : 27.93 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.31), residues: 694 helix: 2.08 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.20 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 529 TYR 0.011 0.001 TYR A 485 PHE 0.038 0.002 PHE A 618 TRP 0.024 0.002 TRP B 799 HIS 0.012 0.002 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 5728) covalent geometry : angle 0.70852 ( 7796) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.83082 ( 8) hydrogen bonds : bond 0.04279 ( 419) hydrogen bonds : angle 4.24250 ( 1257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 GLN cc_start: 0.8837 (tp40) cc_final: 0.8400 (tp40) REVERT: A 709 MET cc_start: 0.8060 (tpp) cc_final: 0.7586 (tpp) REVERT: A 710 ARG cc_start: 0.7452 (mtt180) cc_final: 0.6778 (mtp-110) REVERT: A 764 PHE cc_start: 0.8345 (t80) cc_final: 0.7994 (t80) REVERT: A 775 LYS cc_start: 0.7944 (pttp) cc_final: 0.7713 (pttp) REVERT: A 791 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7353 (t0) REVERT: A 794 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: B 472 GLN cc_start: 0.8850 (tp40) cc_final: 0.8471 (tp40) REVERT: B 585 MET cc_start: 0.8144 (ptt) cc_final: 0.7853 (ptp) REVERT: B 709 MET cc_start: 0.8010 (tpp) cc_final: 0.7490 (tpp) REVERT: B 710 ARG cc_start: 0.7441 (mtt180) cc_final: 0.6765 (mtp-110) REVERT: B 732 PHE cc_start: 0.8705 (m-80) cc_final: 0.8484 (m-80) REVERT: B 775 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7948 (mmmt) REVERT: B 791 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7324 (t0) REVERT: B 811 PHE cc_start: 0.8890 (m-80) cc_final: 0.8664 (m-80) outliers start: 27 outliers final: 16 residues processed: 163 average time/residue: 0.0617 time to fit residues: 13.8579 Evaluate side-chains 165 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 TRP Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 31 optimal weight: 0.0970 chunk 17 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.163408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.134070 restraints weight = 12174.611| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.53 r_work: 0.3899 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5732 Z= 0.136 Angle : 0.702 11.028 7804 Z= 0.344 Chirality : 0.040 0.175 934 Planarity : 0.003 0.026 942 Dihedral : 4.469 21.784 748 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.18 % Allowed : 29.10 % Favored : 67.73 % 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 aren not related in a simple way. whole: 2.10 (0.31), residues: 694 helix: 2.08 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.18 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 529 TYR 0.016 0.001 TYR B 573 PHE 0.052 0.002 PHE A 732 TRP 0.028 0.001 TRP B 799 HIS 0.012 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5728) covalent geometry : angle 0.70215 ( 7796) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.57467 ( 8) hydrogen bonds : bond 0.04094 ( 419) hydrogen bonds : angle 4.19057 ( 1257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 GLN cc_start: 0.8799 (tp40) cc_final: 0.8373 (tp40) REVERT: A 710 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6714 (mtp-110) REVERT: A 764 PHE cc_start: 0.8268 (t80) cc_final: 0.7892 (t80) REVERT: A 775 LYS cc_start: 0.7910 (pttp) cc_final: 0.7158 (mmmt) REVERT: A 791 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7302 (t0) REVERT: A 794 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: B 472 GLN cc_start: 0.8821 (tp40) cc_final: 0.8438 (tp40) REVERT: B 585 MET cc_start: 0.8153 (ptt) cc_final: 0.7870 (ptp) REVERT: B 710 ARG cc_start: 0.7432 (mtt180) cc_final: 0.6634 (mtp-110) REVERT: B 732 PHE cc_start: 0.8641 (m-80) cc_final: 0.8379 (m-80) REVERT: B 775 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7897 (mmmt) REVERT: B 791 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7290 (t0) REVERT: B 794 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7396 (m-30) outliers start: 19 outliers final: 11 residues processed: 160 average time/residue: 0.0610 time to fit residues: 13.6154 Evaluate side-chains 162 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.162749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.133605 restraints weight = 12141.988| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 3.49 r_work: 0.3891 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5732 Z= 0.135 Angle : 0.683 10.407 7804 Z= 0.340 Chirality : 0.041 0.173 934 Planarity : 0.003 0.026 942 Dihedral : 4.392 21.494 748 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.18 % Allowed : 30.10 % Favored : 66.72 % 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 aren not related in a simple way. whole: 2.15 (0.31), residues: 694 helix: 2.09 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.05 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 688 TYR 0.007 0.001 TYR B 717 PHE 0.060 0.002 PHE A 811 TRP 0.033 0.002 TRP B 799 HIS 0.013 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5728) covalent geometry : angle 0.68322 ( 7796) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.53563 ( 8) hydrogen bonds : bond 0.04019 ( 419) hydrogen bonds : angle 4.22114 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1676.83 seconds wall clock time: 29 minutes 29.27 seconds (1769.27 seconds total)