Starting phenix.real_space_refine on Fri Oct 10 17:23:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r33_18859/10_2025/8r33_18859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r33_18859/10_2025/8r33_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r33_18859/10_2025/8r33_18859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r33_18859/10_2025/8r33_18859.map" model { file = "/net/cci-nas-00/data/ceres_data/8r33_18859/10_2025/8r33_18859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r33_18859/10_2025/8r33_18859.cif" } 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-2.0-5842/lib/python3.9/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: 2.44, per 1000 atoms: 0.30 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: 0.87 Conformation dependent library (CDL) restraints added in 258.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.25 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: 1.20 Time building geometry restraints manager: 1.06 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 - 18.00: 4021 18.00 - 36.00: 523 36.00 - 54.00: 194 54.00 - 72.00: 36 72.00 - 89.99: 6 Dihedral angle restraints: 4780 sinusoidal: 1974 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 4777 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: 0.02 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: 12.020 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.580 Find NCS groups from input model: 0.130 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:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 18.607 89.995 2972 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 aren 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 covalent geometry : bond 0.00280 ( 7890) covalent geometry : angle 0.55664 (10634) hydrogen bonds : bond 0.18053 ( 531) hydrogen bonds : angle 7.03763 ( 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 : 0.345 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: 0.6275 time to fit residues: 71.0961 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 : 0.307 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3615 r_free = 0.3615 target = 0.133262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106553 restraints weight = 7895.544| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.26 r_work: 0.3170 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0987 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= 0.183 Angle : 0.605 6.111 10634 Z= 0.317 Chirality : 0.041 0.148 1270 Planarity : 0.005 0.044 1238 Dihedral : 15.674 80.916 1389 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.27 % Allowed : 18.14 % Favored : 78.59 % 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: 2.03 (0.27), residues: 970 helix: 1.83 (0.19), residues: 728 sheet: -0.17 (1.03), residues: 24 loop : -0.03 (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 0.025 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 covalent geometry : bond 0.00409 ( 7890) covalent geometry : angle 0.60543 (10634) hydrogen bonds : bond 0.05592 ( 531) hydrogen bonds : angle 5.15451 ( 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 115 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.329 Fit side-chains REVERT: A 657 LYS cc_start: 0.7351 (mmpt) cc_final: 0.7148 (mmtm) REVERT: B 566 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7875 (tp) REVERT: B 647 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7373 (mppt) outliers start: 26 outliers final: 8 residues processed: 110 average time/residue: 0.6659 time to fit residues: 77.4259 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 : 0.306 ------------------------------------------------------------------------------- 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: 4.9990 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105374 restraints weight = 7920.982| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.25 r_work: 0.3151 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1130 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= 0.195 Angle : 0.613 6.680 10634 Z= 0.319 Chirality : 0.042 0.155 1270 Planarity : 0.004 0.043 1238 Dihedral : 15.408 70.235 1376 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.39 % Allowed : 18.51 % Favored : 79.09 % 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: 2.01 (0.27), residues: 970 helix: 1.80 (0.19), residues: 728 sheet: -0.21 (1.01), residues: 24 loop : 0.03 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 836 TYR 0.020 0.002 TYR A 518 PHE 0.025 0.002 PHE B 643 TRP 0.012 0.001 TRP A 721 HIS 0.009 0.002 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7890) covalent geometry : angle 0.61285 (10634) hydrogen bonds : bond 0.05612 ( 531) hydrogen bonds : angle 5.09948 ( 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 110 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.333 Fit side-chains REVERT: B 647 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7403 (mppt) REVERT: B 770 MET cc_start: 0.8255 (mtp) cc_final: 0.8039 (mtp) outliers start: 19 outliers final: 9 residues processed: 104 average time/residue: 0.6746 time to fit residues: 74.1473 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 : 0.370 ------------------------------------------------------------------------------- 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 662 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106584 restraints weight = 8073.981| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.28 r_work: 0.3171 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7890 Z= 0.158 Angle : 0.573 5.763 10634 Z= 0.297 Chirality : 0.040 0.148 1270 Planarity : 0.004 0.042 1238 Dihedral : 14.812 64.057 1372 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.77 % Allowed : 17.38 % Favored : 79.85 % 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: 2.21 (0.27), residues: 970 helix: 1.96 (0.19), residues: 728 sheet: -0.17 (1.03), residues: 24 loop : 0.08 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 840 TYR 0.018 0.001 TYR A 518 PHE 0.025 0.002 PHE B 643 TRP 0.010 0.001 TRP A 721 HIS 0.007 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7890) covalent geometry : angle 0.57318 (10634) hydrogen bonds : bond 0.04995 ( 531) hydrogen bonds : angle 4.89823 ( 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 112 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.310 Fit side-chains REVERT: A 657 LYS cc_start: 0.7279 (mmpt) cc_final: 0.7030 (mmtm) REVERT: A 770 MET cc_start: 0.8166 (mtp) cc_final: 0.7842 (mtt) REVERT: B 647 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7389 (mppt) REVERT: B 657 LYS cc_start: 0.7294 (mmpt) cc_final: 0.7079 (mmtm) REVERT: B 770 MET cc_start: 0.8199 (mtp) cc_final: 0.7936 (mtp) outliers start: 22 outliers final: 9 residues processed: 107 average time/residue: 0.6279 time to fit residues: 71.1173 Evaluate side-chains 99 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105867 restraints weight = 8016.164| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.27 r_work: 0.3160 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1271 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= 0.173 Angle : 0.587 6.029 10634 Z= 0.305 Chirality : 0.041 0.151 1270 Planarity : 0.004 0.043 1238 Dihedral : 14.710 60.405 1368 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.52 % Allowed : 18.01 % 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 aren not related in a simple way. whole: 2.14 (0.27), residues: 970 helix: 1.91 (0.19), residues: 728 sheet: -0.28 (1.02), residues: 24 loop : 0.05 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 840 TYR 0.019 0.001 TYR A 518 PHE 0.025 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 covalent geometry : bond 0.00391 ( 7890) covalent geometry : angle 0.58685 (10634) hydrogen bonds : bond 0.05185 ( 531) hydrogen bonds : angle 4.93793 ( 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 110 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.319 Fit side-chains REVERT: A 657 LYS cc_start: 0.7301 (mmpt) cc_final: 0.7015 (mmtm) REVERT: B 647 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7388 (mppt) REVERT: B 657 LYS cc_start: 0.7319 (mmpt) cc_final: 0.7078 (mmtm) REVERT: B 770 MET cc_start: 0.8226 (mtp) cc_final: 0.8005 (mtp) outliers start: 20 outliers final: 10 residues processed: 105 average time/residue: 0.6504 time to fit residues: 72.3554 Evaluate side-chains 100 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108499 restraints weight = 7947.557| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.27 r_work: 0.3198 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1380 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= 0.130 Angle : 0.530 5.190 10634 Z= 0.274 Chirality : 0.038 0.140 1270 Planarity : 0.004 0.043 1238 Dihedral : 14.079 59.747 1368 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.76 % Allowed : 18.64 % 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 aren not related in a simple way. whole: 2.45 (0.27), residues: 970 helix: 2.15 (0.19), residues: 726 sheet: -0.07 (1.05), residues: 24 loop : 0.13 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 840 TYR 0.015 0.001 TYR A 518 PHE 0.024 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 covalent geometry : bond 0.00279 ( 7890) covalent geometry : angle 0.53037 (10634) hydrogen bonds : bond 0.04391 ( 531) hydrogen bonds : angle 4.69023 ( 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 104 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.328 Fit side-chains REVERT: A 497 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8119 (mtm) REVERT: A 651 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7777 (p) REVERT: A 657 LYS cc_start: 0.7237 (mmpt) cc_final: 0.6956 (mmtm) REVERT: A 770 MET cc_start: 0.8155 (mtp) cc_final: 0.7747 (mtm) REVERT: B 651 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7813 (p) REVERT: B 657 LYS cc_start: 0.7267 (mmpt) cc_final: 0.7039 (mmtm) outliers start: 14 outliers final: 6 residues processed: 101 average time/residue: 0.6399 time to fit residues: 68.4899 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 MET 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 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: 0.2980 chunk 49 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108990 restraints weight = 8026.812| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.27 r_work: 0.3204 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7890 Z= 0.126 Angle : 0.523 5.143 10634 Z= 0.270 Chirality : 0.038 0.140 1270 Planarity : 0.004 0.041 1238 Dihedral : 13.647 59.124 1368 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.89 % Allowed : 18.51 % 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 aren not related in a simple way. whole: 2.58 (0.27), residues: 970 helix: 2.26 (0.19), residues: 722 sheet: 0.02 (1.06), residues: 24 loop : 0.14 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 840 TYR 0.015 0.001 TYR A 518 PHE 0.024 0.001 PHE A 643 TRP 0.008 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7890) covalent geometry : angle 0.52307 (10634) hydrogen bonds : bond 0.04299 ( 531) hydrogen bonds : angle 4.62332 ( 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 104 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.297 Fit side-chains REVERT: A 402 ASN cc_start: 0.5568 (OUTLIER) cc_final: 0.5279 (p0) REVERT: A 497 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8130 (mtm) REVERT: A 651 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7765 (p) REVERT: A 657 LYS cc_start: 0.7228 (mmpt) cc_final: 0.6922 (mmtm) REVERT: A 770 MET cc_start: 0.8159 (mtp) cc_final: 0.7730 (mtm) REVERT: B 651 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7794 (p) REVERT: B 657 LYS cc_start: 0.7239 (mmpt) cc_final: 0.7014 (mmtm) REVERT: B 753 LYS cc_start: 0.7364 (pttt) cc_final: 0.7043 (ptmm) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 0.6397 time to fit residues: 68.5978 Evaluate side-chains 100 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 497 MET Chi-restraints excluded: chain A residue 651 THR 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 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: 0.6980 chunk 31 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107781 restraints weight = 7971.982| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.26 r_work: 0.3184 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1413 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= 0.147 Angle : 0.549 5.627 10634 Z= 0.284 Chirality : 0.039 0.146 1270 Planarity : 0.004 0.042 1238 Dihedral : 13.685 59.061 1367 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.76 % Allowed : 18.26 % Favored : 79.97 % 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 aren not related in a simple way. whole: 2.46 (0.27), residues: 970 helix: 2.12 (0.19), residues: 728 sheet: 0.12 (1.06), residues: 24 loop : 0.19 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 840 TYR 0.017 0.001 TYR A 518 PHE 0.024 0.001 PHE B 643 TRP 0.009 0.001 TRP A 721 HIS 0.007 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7890) covalent geometry : angle 0.54863 (10634) hydrogen bonds : bond 0.04658 ( 531) hydrogen bonds : angle 4.71524 ( 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 103 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.309 Fit side-chains REVERT: A 651 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7781 (p) REVERT: A 657 LYS cc_start: 0.7228 (mmpt) cc_final: 0.6920 (mmtm) REVERT: A 770 MET cc_start: 0.8190 (mtp) cc_final: 0.7747 (mtm) REVERT: B 647 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7392 (mppt) REVERT: B 651 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7802 (p) REVERT: B 753 LYS cc_start: 0.7358 (pttt) cc_final: 0.7045 (ptmm) REVERT: B 770 MET cc_start: 0.8237 (mtp) cc_final: 0.8011 (mtp) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.6525 time to fit residues: 69.1891 Evaluate side-chains 99 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 651 THR 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: 2.9990 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 0.0670 chunk 78 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110049 restraints weight = 7972.838| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.27 r_work: 0.3217 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7890 Z= 0.120 Angle : 0.523 6.753 10634 Z= 0.268 Chirality : 0.038 0.136 1270 Planarity : 0.004 0.041 1238 Dihedral : 13.209 58.948 1367 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.39 % Allowed : 18.77 % Favored : 79.85 % 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: 2.66 (0.27), residues: 970 helix: 2.31 (0.19), residues: 722 sheet: 0.23 (1.08), residues: 24 loop : 0.16 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 840 TYR 0.014 0.001 TYR B 518 PHE 0.023 0.001 PHE B 643 TRP 0.007 0.001 TRP A 721 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7890) covalent geometry : angle 0.52252 (10634) hydrogen bonds : bond 0.04105 ( 531) hydrogen bonds : angle 4.54586 ( 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 100 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.314 Fit side-chains REVERT: A 651 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7752 (p) REVERT: A 657 LYS cc_start: 0.7204 (mmpt) cc_final: 0.6895 (mmtm) REVERT: A 770 MET cc_start: 0.8146 (mtp) cc_final: 0.7700 (mtm) REVERT: B 647 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7388 (mppt) REVERT: B 651 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7785 (p) REVERT: B 657 LYS cc_start: 0.7206 (mmpt) cc_final: 0.6972 (mmtm) REVERT: B 753 LYS cc_start: 0.7373 (pttt) cc_final: 0.7062 (ptmm) REVERT: B 770 MET cc_start: 0.8190 (mtp) cc_final: 0.7970 (mtp) outliers start: 11 outliers final: 5 residues processed: 98 average time/residue: 0.6864 time to fit residues: 71.0338 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 : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 651 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104397 restraints weight = 7947.657| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.27 r_work: 0.3138 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7890 Z= 0.238 Angle : 0.669 7.583 10634 Z= 0.345 Chirality : 0.044 0.162 1270 Planarity : 0.004 0.043 1238 Dihedral : 14.438 59.447 1366 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.26 % Allowed : 19.02 % Favored : 79.72 % 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: 2.02 (0.27), residues: 970 helix: 1.83 (0.19), residues: 724 sheet: -0.05 (1.01), residues: 24 loop : -0.02 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 440 TYR 0.023 0.002 TYR A 518 PHE 0.026 0.002 PHE B 643 TRP 0.014 0.002 TRP A 721 HIS 0.012 0.002 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 7890) covalent geometry : angle 0.66859 (10634) hydrogen bonds : bond 0.05866 ( 531) hydrogen bonds : angle 5.07935 ( 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 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.286 Fit side-chains REVERT: A 651 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 770 MET cc_start: 0.8268 (mtp) cc_final: 0.7951 (mtt) REVERT: B 647 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7401 (mppt) REVERT: B 657 LYS cc_start: 0.7281 (mmpt) cc_final: 0.6970 (mmtm) REVERT: B 753 LYS cc_start: 0.7352 (pttt) cc_final: 0.7013 (ptmm) REVERT: B 770 MET cc_start: 0.8297 (mtp) cc_final: 0.8056 (mtp) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.6671 time to fit residues: 67.2315 Evaluate side-chains 94 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 651 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108257 restraints weight = 7941.141| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.26 r_work: 0.3194 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7890 Z= 0.135 Angle : 0.555 6.523 10634 Z= 0.284 Chirality : 0.038 0.141 1270 Planarity : 0.004 0.042 1238 Dihedral : 13.673 59.827 1366 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.13 % Allowed : 19.52 % 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 aren not related in a simple way. whole: 2.41 (0.27), residues: 970 helix: 2.11 (0.19), residues: 728 sheet: 0.16 (1.06), residues: 24 loop : 0.10 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 840 TYR 0.015 0.001 TYR A 518 PHE 0.023 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 covalent geometry : bond 0.00295 ( 7890) covalent geometry : angle 0.55547 (10634) hydrogen bonds : bond 0.04459 ( 531) hydrogen bonds : angle 4.68567 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.08 seconds wall clock time: 58 minutes 1.69 seconds (3481.69 seconds total)