Starting phenix.real_space_refine on Wed Mar 12 16:21:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r33_18859/03_2025/8r33_18859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r33_18859/03_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_18859/03_2025/8r33_18859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r33_18859/03_2025/8r33_18859.map" model { file = "/net/cci-nas-00/data/ceres_data/8r33_18859/03_2025/8r33_18859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r33_18859/03_2025/8r33_18859.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.72, per 1000 atoms: 0.96 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: 2.30 Conformation dependent library (CDL) restraints added in 987.1 milliseconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 79.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 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: 2.71 Time building geometry restraints manager: 2.67 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: 0.04 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: 69.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.720 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.780 ------------------------------------------------------------------------------- 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= 0.181 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (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 TRP 0.006 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 PHE 0.021 0.001 PHE A 643 TYR 0.013 0.002 TYR A 518 ARG 0.002 0.000 ARG A 836 *********************** 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 : 0.836 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: 1.3090 time to fit residues: 148.4337 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 : 0.909 ------------------------------------------------------------------------------- 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 81 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** B 606 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 = 0.3631 r_free = 0.3631 target = 0.134687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108049 restraints weight = 7874.417| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.26 r_work: 0.3190 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0982 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= 0.214 Angle : 0.567 5.167 10634 Z= 0.297 Chirality : 0.039 0.144 1270 Planarity : 0.004 0.044 1238 Dihedral : 15.392 80.741 1389 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.02 % Allowed : 18.26 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.27), residues: 970 helix: 1.98 (0.19), residues: 724 sheet: -0.07 (1.05), residues: 24 loop : -0.11 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 721 HIS 0.007 0.001 HIS A 439 PHE 0.025 0.002 PHE B 643 TYR 0.015 0.002 TYR A 518 ARG 0.002 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.842 Fit side-chains REVERT: A 497 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: B 647 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7349 (mppt) REVERT: B 748 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7989 (ttmm) outliers start: 24 outliers final: 9 residues processed: 109 average time/residue: 1.3382 time to fit residues: 154.5699 Evaluate side-chains 100 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 MET 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 402 ASN 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 748 LYS 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 1 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 0.0070 chunk 89 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.107147 restraints weight = 7986.910| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.26 r_work: 0.3175 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7890 Z= 0.223 Angle : 0.563 5.355 10634 Z= 0.293 Chirality : 0.040 0.149 1270 Planarity : 0.004 0.043 1238 Dihedral : 14.778 69.032 1374 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.27 % Allowed : 18.51 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.27), residues: 970 helix: 1.97 (0.19), residues: 728 sheet: 0.19 (1.04), residues: 24 loop : 0.10 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 721 HIS 0.008 0.002 HIS A 439 PHE 0.026 0.002 PHE B 643 TYR 0.018 0.001 TYR A 518 ARG 0.002 0.000 ARG B 836 *********************** 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 109 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.923 Fit side-chains REVERT: B 647 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7386 (mppt) REVERT: B 770 MET cc_start: 0.8207 (mtp) cc_final: 0.8004 (mtp) outliers start: 18 outliers final: 7 residues processed: 105 average time/residue: 1.3521 time to fit residues: 150.2185 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 : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 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 56 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.133218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106454 restraints weight = 7913.884| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.27 r_work: 0.3167 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7890 Z= 0.243 Angle : 0.580 6.016 10634 Z= 0.301 Chirality : 0.040 0.149 1270 Planarity : 0.004 0.042 1238 Dihedral : 14.572 63.164 1368 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.27 % Allowed : 17.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.27), residues: 970 helix: 1.95 (0.19), residues: 728 sheet: 0.12 (1.02), residues: 24 loop : 0.14 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 721 HIS 0.008 0.002 HIS A 439 PHE 0.025 0.002 PHE B 643 TYR 0.019 0.001 TYR A 518 ARG 0.001 0.000 ARG A 836 *********************** 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 108 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.841 Fit side-chains REVERT: A 657 LYS cc_start: 0.7290 (mmpt) cc_final: 0.7038 (mmtm) REVERT: A 770 MET cc_start: 0.8193 (mtp) cc_final: 0.7777 (mtm) REVERT: B 647 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7392 (mppt) REVERT: B 770 MET cc_start: 0.8218 (mtp) cc_final: 0.7947 (mtp) outliers start: 18 outliers final: 9 residues processed: 104 average time/residue: 1.3327 time to fit residues: 146.9497 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 : 0.706 ------------------------------------------------------------------------------- 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 A residue 873 VAL Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.134814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108151 restraints weight = 7870.607| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.27 r_work: 0.3193 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7890 Z= 0.195 Angle : 0.539 5.427 10634 Z= 0.279 Chirality : 0.039 0.143 1270 Planarity : 0.004 0.041 1238 Dihedral : 14.109 59.784 1368 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.14 % Allowed : 17.63 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.27), residues: 970 helix: 2.11 (0.19), residues: 728 sheet: 0.23 (1.04), residues: 24 loop : 0.15 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.016 0.001 TYR A 518 ARG 0.002 0.000 ARG A 840 *********************** 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 107 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.879 Fit side-chains REVERT: A 651 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7766 (p) REVERT: A 657 LYS cc_start: 0.7268 (mmpt) cc_final: 0.7008 (mmtm) REVERT: A 770 MET cc_start: 0.8190 (mtp) cc_final: 0.7868 (mtt) REVERT: B 651 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7817 (p) outliers start: 17 outliers final: 7 residues processed: 102 average time/residue: 1.2948 time to fit residues: 140.0449 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 : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.133456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106835 restraints weight = 7916.175| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.26 r_work: 0.3171 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7890 Z= 0.227 Angle : 0.564 5.813 10634 Z= 0.292 Chirality : 0.040 0.149 1270 Planarity : 0.004 0.042 1238 Dihedral : 14.129 59.574 1368 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.27 % Allowed : 17.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.27), residues: 970 helix: 2.03 (0.19), residues: 728 sheet: 0.07 (1.01), residues: 24 loop : 0.17 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 721 HIS 0.008 0.002 HIS A 439 PHE 0.025 0.002 PHE B 643 TYR 0.019 0.001 TYR A 518 ARG 0.003 0.000 ARG A 840 *********************** 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 108 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.818 Fit side-chains REVERT: A 651 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7782 (p) REVERT: A 657 LYS cc_start: 0.7269 (mmpt) cc_final: 0.6993 (mmtm) REVERT: B 647 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7393 (mppt) REVERT: B 651 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7803 (p) outliers start: 18 outliers final: 8 residues processed: 105 average time/residue: 1.3017 time to fit residues: 144.9032 Evaluate side-chains 99 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106945 restraints weight = 7930.069| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.26 r_work: 0.3175 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1353 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= 0.228 Angle : 0.570 5.978 10634 Z= 0.294 Chirality : 0.040 0.148 1270 Planarity : 0.004 0.041 1238 Dihedral : 14.031 59.474 1368 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.39 % Allowed : 17.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.27), residues: 970 helix: 2.02 (0.19), residues: 728 sheet: 0.02 (1.00), residues: 24 loop : 0.16 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 721 HIS 0.008 0.002 HIS A 439 PHE 0.025 0.001 PHE B 643 TYR 0.018 0.001 TYR A 518 ARG 0.002 0.000 ARG A 840 *********************** 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 108 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.822 Fit side-chains REVERT: A 651 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7780 (p) REVERT: A 657 LYS cc_start: 0.7269 (mmpt) cc_final: 0.6985 (mmtm) REVERT: A 770 MET cc_start: 0.8176 (mtp) cc_final: 0.7730 (mtm) REVERT: B 647 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7390 (mppt) REVERT: B 651 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7815 (p) REVERT: B 657 LYS cc_start: 0.7271 (mmpt) cc_final: 0.6973 (mmtt) REVERT: B 770 MET cc_start: 0.8167 (mtp) cc_final: 0.7732 (mtm) outliers start: 19 outliers final: 9 residues processed: 105 average time/residue: 1.3186 time to fit residues: 146.9616 Evaluate side-chains 101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 611 SER Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.134271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107740 restraints weight = 7922.440| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.25 r_work: 0.3185 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7890 Z= 0.205 Angle : 0.553 5.542 10634 Z= 0.285 Chirality : 0.039 0.144 1270 Planarity : 0.004 0.041 1238 Dihedral : 13.802 59.465 1368 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.27), residues: 970 helix: 2.09 (0.19), residues: 728 sheet: 0.01 (1.01), residues: 24 loop : 0.16 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 721 HIS 0.007 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.017 0.001 TYR B 518 ARG 0.002 0.000 ARG A 840 *********************** 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 105 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.894 Fit side-chains REVERT: A 651 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7771 (p) REVERT: A 657 LYS cc_start: 0.7272 (mmpt) cc_final: 0.6981 (mmtm) REVERT: A 770 MET cc_start: 0.8166 (mtp) cc_final: 0.7716 (mtm) REVERT: B 647 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7389 (mppt) REVERT: B 651 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7802 (p) REVERT: B 657 LYS cc_start: 0.7286 (mmpt) cc_final: 0.6998 (mmtm) REVERT: B 753 LYS cc_start: 0.7314 (pttt) cc_final: 0.6992 (ptmm) REVERT: B 770 MET cc_start: 0.8176 (mtp) cc_final: 0.7741 (mtm) outliers start: 15 outliers final: 8 residues processed: 102 average time/residue: 1.3251 time to fit residues: 143.2543 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 : 0.819 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.134691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108019 restraints weight = 8048.896| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.28 r_work: 0.3191 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7890 Z= 0.198 Angle : 0.546 5.416 10634 Z= 0.281 Chirality : 0.038 0.143 1270 Planarity : 0.004 0.041 1238 Dihedral : 13.602 59.374 1368 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.51 % Allowed : 19.14 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.27), residues: 970 helix: 2.13 (0.19), residues: 728 sheet: 0.00 (1.01), residues: 24 loop : 0.18 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.016 0.001 TYR A 518 ARG 0.002 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.952 Fit side-chains REVERT: A 651 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7779 (p) REVERT: A 657 LYS cc_start: 0.7211 (mmpt) cc_final: 0.6915 (mmtm) REVERT: A 770 MET cc_start: 0.8163 (mtp) cc_final: 0.7756 (mtm) REVERT: B 647 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7380 (mppt) REVERT: B 651 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7812 (p) REVERT: B 657 LYS cc_start: 0.7297 (mmpt) cc_final: 0.7035 (mmtm) REVERT: B 753 LYS cc_start: 0.7303 (pttt) cc_final: 0.6993 (ptmm) REVERT: B 770 MET cc_start: 0.8166 (mtp) cc_final: 0.7735 (mtm) outliers start: 12 outliers final: 7 residues processed: 99 average time/residue: 1.5652 time to fit residues: 163.9377 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 : 0.953 ------------------------------------------------------------------------------- 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 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 873 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.134945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108358 restraints weight = 7941.826| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.27 r_work: 0.3197 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1430 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= 0.191 Angle : 0.542 5.566 10634 Z= 0.279 Chirality : 0.038 0.142 1270 Planarity : 0.004 0.041 1238 Dihedral : 13.402 59.285 1365 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.13 % Allowed : 19.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.27), residues: 970 helix: 2.17 (0.19), residues: 726 sheet: 0.05 (1.03), residues: 24 loop : 0.23 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.017 0.001 TYR A 518 ARG 0.001 0.000 ARG A 836 ********************** 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 98 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.714 Fit side-chains REVERT: A 651 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7772 (p) REVERT: A 657 LYS cc_start: 0.7214 (mmpt) cc_final: 0.6873 (mmtm) REVERT: A 770 MET cc_start: 0.8168 (mtp) cc_final: 0.7756 (mtm) REVERT: B 647 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7381 (mppt) REVERT: B 651 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7801 (p) REVERT: B 657 LYS cc_start: 0.7285 (mmpt) cc_final: 0.7007 (mmtm) REVERT: B 753 LYS cc_start: 0.7321 (pttt) cc_final: 0.7031 (ptmm) REVERT: B 770 MET cc_start: 0.8158 (mtp) cc_final: 0.7730 (mtm) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 1.3929 time to fit residues: 142.1909 Evaluate side-chains 98 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 67 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.135214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108622 restraints weight = 7962.323| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.27 r_work: 0.3200 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1489 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= 0.186 Angle : 0.537 5.748 10634 Z= 0.276 Chirality : 0.038 0.141 1270 Planarity : 0.004 0.041 1238 Dihedral : 13.231 59.222 1364 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.26 % Allowed : 19.14 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.27), residues: 970 helix: 2.19 (0.19), residues: 726 sheet: 0.05 (1.03), residues: 24 loop : 0.25 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 721 HIS 0.006 0.001 HIS A 439 PHE 0.024 0.001 PHE B 643 TYR 0.016 0.001 TYR B 518 ARG 0.001 0.000 ARG A 836 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7623.94 seconds wall clock time: 132 minutes 59.57 seconds (7979.57 seconds total)