Starting phenix.real_space_refine on Sun Dec 29 05:18:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2q_27146/12_2024/8d2q_27146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2q_27146/12_2024/8d2q_27146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2q_27146/12_2024/8d2q_27146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2q_27146/12_2024/8d2q_27146.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2q_27146/12_2024/8d2q_27146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2q_27146/12_2024/8d2q_27146.cif" } resolution = 2.58 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 121 5.49 5 Mg 5 5.21 5 S 17 5.16 5 C 5643 2.51 5 N 1817 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9721 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7143 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 849} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1835 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 36} Link IDs: {'rna2p': 11, 'rna3p': 74} Chain breaks: 2 Chain: "T" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 10} Chain: "X" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.54, per 1000 atoms: 0.67 Number of scatterers: 9721 At special positions: 0 Unit cell: (96.525, 109.725, 119.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 P 121 15.00 Mg 5 11.99 O 2118 8.00 N 1817 7.00 C 5643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 610 " distance=2.04 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 613 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 43.6% alpha, 10.7% beta 44 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.574A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 524 through 552 removed outlier: 3.848A pdb=" N ALA A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 572 Processing helix chain 'A' and resid 636 through 643 Processing helix chain 'A' and resid 653 through 669 removed outlier: 3.607A pdb=" N SER A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 703 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 782 removed outlier: 4.417A pdb=" N PHE A 780 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 820 removed outlier: 3.707A pdb=" N ARG A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 981 through 986 Processing helix chain 'A' and resid 988 through 997 Processing helix chain 'A' and resid 1024 through 1033 removed outlier: 3.992A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1071 Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1094 through 1098 Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 711 removed outlier: 6.343A pdb=" N ILE A 513 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 710 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 515 " --> pdb=" O PHE A 710 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 24 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER A 44 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 26 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 42 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 28 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 824 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 590 through 591 removed outlier: 3.726A pdb=" N ASP A 590 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA4, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA5, first strand: chain 'A' and resid 899 through 900 Processing sheet with id=AA6, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA7, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.641A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.527A pdb=" N ARG A1048 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE A1043 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 5.22 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2206 1.33 - 1.46: 2986 1.46 - 1.58: 4720 1.58 - 1.70: 240 1.70 - 1.82: 24 Bond restraints: 10176 Sorted by residual: bond pdb=" CG PRO A 487 " pdb=" CD PRO A 487 " ideal model delta sigma weight residual 1.503 1.315 0.188 3.40e-02 8.65e+02 3.05e+01 bond pdb=" C1' DT T 23 " pdb=" N1 DT T 23 " ideal model delta sigma weight residual 1.490 1.607 -0.117 3.00e-02 1.11e+03 1.53e+01 bond pdb=" CG PRO A 476 " pdb=" CD PRO A 476 " ideal model delta sigma weight residual 1.503 1.391 0.112 3.40e-02 8.65e+02 1.09e+01 bond pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.06e+01 bond pdb=" C3' DT T 22 " pdb=" O3' DT T 22 " ideal model delta sigma weight residual 1.422 1.518 -0.096 3.00e-02 1.11e+03 1.03e+01 ... (remaining 10171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 14060 2.87 - 5.75: 255 5.75 - 8.62: 38 8.62 - 11.50: 8 11.50 - 14.37: 5 Bond angle restraints: 14366 Sorted by residual: angle pdb=" CA PRO A 487 " pdb=" N PRO A 487 " pdb=" CD PRO A 487 " ideal model delta sigma weight residual 112.00 97.63 14.37 1.40e+00 5.10e-01 1.05e+02 angle pdb=" N PRO A 487 " pdb=" CD PRO A 487 " pdb=" CG PRO A 487 " ideal model delta sigma weight residual 103.20 89.19 14.01 1.50e+00 4.44e-01 8.73e+01 angle pdb=" C3' A B 12 " pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 120.20 133.24 -13.04 1.50e+00 4.44e-01 7.56e+01 angle pdb=" C PRO A 675 " pdb=" N GLU A 676 " pdb=" CA GLU A 676 " ideal model delta sigma weight residual 121.70 134.99 -13.29 1.80e+00 3.09e-01 5.45e+01 angle pdb=" N GLU A1067 " pdb=" CA GLU A1067 " pdb=" CB GLU A1067 " ideal model delta sigma weight residual 110.12 120.81 -10.69 1.47e+00 4.63e-01 5.28e+01 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 5612 31.09 - 62.17: 457 62.17 - 93.26: 103 93.26 - 124.34: 3 124.34 - 155.43: 4 Dihedral angle restraints: 6179 sinusoidal: 3563 harmonic: 2616 Sorted by residual: dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -5.03 -80.97 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS A 578 " pdb=" SG CYS A 578 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -166.52 80.52 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -162.59 76.59 1 1.00e+01 1.00e-02 7.37e+01 ... (remaining 6176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1450 0.076 - 0.151: 177 0.151 - 0.227: 19 0.227 - 0.303: 5 0.303 - 0.378: 2 Chirality restraints: 1653 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA GLU A1067 " pdb=" N GLU A1067 " pdb=" C GLU A1067 " pdb=" CB GLU A1067 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C1' A B 12 " pdb=" O4' A B 12 " pdb=" C2' A B 12 " pdb=" N9 A B 12 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1650 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 486 " 0.082 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 487 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 22 " 0.032 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" N1 DT T 22 " -0.068 2.00e-02 2.50e+03 pdb=" C2 DT T 22 " 0.025 2.00e-02 2.50e+03 pdb=" O2 DT T 22 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT T 22 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT T 22 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT T 22 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DT T 22 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT T 22 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DT T 22 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1063 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C VAL A1063 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL A1063 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A1064 " 0.018 2.00e-02 2.50e+03 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 281 2.67 - 3.23: 8105 3.23 - 3.79: 18047 3.79 - 4.34: 23052 4.34 - 4.90: 34466 Nonbonded interactions: 83951 Sorted by model distance: nonbonded pdb=" OD2 ASP A 18 " pdb="MG MG A1201 " model vdw 2.113 2.170 nonbonded pdb=" ND1 HIS A 750 " pdb="MG MG A1201 " model vdw 2.158 2.250 nonbonded pdb=" OP1 C B 52 " pdb="MG MG B 204 " model vdw 2.241 2.170 nonbonded pdb=" OG SER A 59 " pdb=" OP1 C B 17 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR A 684 " pdb=" OP1 DT T 23 " model vdw 2.256 3.040 ... (remaining 83946 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.660 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.006 0.188 10176 Z= 0.364 Angle : 0.974 14.373 14366 Z= 0.525 Chirality : 0.052 0.378 1653 Planarity : 0.009 0.115 1420 Dihedral : 20.817 155.427 4468 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.68 (0.25), residues: 898 helix: -1.09 (0.23), residues: 397 sheet: -0.27 (0.54), residues: 85 loop : -1.19 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 942 HIS 0.007 0.002 HIS A 574 PHE 0.047 0.003 PHE A 76 TYR 0.023 0.002 TYR A 698 ARG 0.021 0.001 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.970 Fit side-chains REVERT: A 487 PRO cc_start: 0.6995 (Cg_exo) cc_final: 0.6628 (Cg_endo) REVERT: A 804 LYS cc_start: 0.8030 (tttp) cc_final: 0.7803 (tppt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.7893 time to fit residues: 136.2585 Evaluate side-chains 57 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 802 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10176 Z= 0.204 Angle : 0.612 7.751 14366 Z= 0.319 Chirality : 0.039 0.308 1653 Planarity : 0.005 0.043 1420 Dihedral : 22.203 155.130 2766 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.94 % Allowed : 5.26 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 898 helix: 0.46 (0.25), residues: 395 sheet: -0.33 (0.53), residues: 84 loop : -0.87 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 145 HIS 0.005 0.001 HIS A 749 PHE 0.025 0.002 PHE A 76 TYR 0.011 0.001 TYR A 986 ARG 0.008 0.000 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.814 Fit side-chains REVERT: A 576 MET cc_start: 0.1697 (OUTLIER) cc_final: 0.1250 (mmt) REVERT: A 805 GLU cc_start: 0.7194 (tp30) cc_final: 0.6600 (tp30) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 1.4724 time to fit residues: 104.2099 Evaluate side-chains 61 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 0.0570 chunk 31 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 802 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10176 Z= 0.286 Angle : 0.654 8.145 14366 Z= 0.338 Chirality : 0.041 0.316 1653 Planarity : 0.006 0.043 1420 Dihedral : 22.208 160.748 2766 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.48 % Allowed : 6.87 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.27), residues: 898 helix: 0.95 (0.26), residues: 397 sheet: -0.40 (0.53), residues: 84 loop : -0.78 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.007 0.001 HIS A 486 PHE 0.029 0.002 PHE A 76 TYR 0.018 0.002 TYR A 698 ARG 0.007 0.001 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8254 (mt0) cc_final: 0.7865 (mt0) REVERT: A 576 MET cc_start: 0.1839 (OUTLIER) cc_final: 0.1499 (mmt) REVERT: A 802 GLN cc_start: 0.6866 (tp40) cc_final: 0.6556 (tt0) REVERT: A 805 GLU cc_start: 0.7192 (tp30) cc_final: 0.6598 (tp30) outliers start: 11 outliers final: 4 residues processed: 65 average time/residue: 1.5719 time to fit residues: 108.9218 Evaluate side-chains 61 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10176 Z= 0.293 Angle : 0.650 7.831 14366 Z= 0.337 Chirality : 0.042 0.311 1653 Planarity : 0.006 0.045 1420 Dihedral : 22.190 162.661 2766 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.02 % Allowed : 9.30 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 898 helix: 1.00 (0.26), residues: 398 sheet: -0.35 (0.56), residues: 79 loop : -0.70 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 145 HIS 0.005 0.001 HIS A 486 PHE 0.029 0.002 PHE A 76 TYR 0.020 0.002 TYR A 698 ARG 0.004 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8240 (mt0) cc_final: 0.7805 (mt0) REVERT: A 805 GLU cc_start: 0.7172 (tp30) cc_final: 0.6584 (tp30) outliers start: 15 outliers final: 7 residues processed: 66 average time/residue: 1.5879 time to fit residues: 111.7301 Evaluate side-chains 61 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10176 Z= 0.339 Angle : 0.694 8.256 14366 Z= 0.357 Chirality : 0.044 0.321 1653 Planarity : 0.006 0.052 1420 Dihedral : 22.229 161.775 2766 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.29 % Allowed : 11.05 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.27), residues: 898 helix: 0.94 (0.26), residues: 398 sheet: -0.52 (0.56), residues: 84 loop : -0.76 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 184 HIS 0.004 0.001 HIS A 936 PHE 0.031 0.002 PHE A 76 TYR 0.023 0.002 TYR A 698 ARG 0.013 0.001 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8251 (mt0) cc_final: 0.7824 (mt0) REVERT: A 805 GLU cc_start: 0.7158 (tp30) cc_final: 0.6553 (tp30) REVERT: A 895 GLU cc_start: 0.6440 (mp0) cc_final: 0.6009 (pm20) outliers start: 17 outliers final: 9 residues processed: 71 average time/residue: 1.5868 time to fit residues: 119.9204 Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 946 HIS A1060 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10176 Z= 0.350 Angle : 0.697 8.899 14366 Z= 0.360 Chirality : 0.044 0.320 1653 Planarity : 0.006 0.054 1420 Dihedral : 22.207 160.661 2766 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.10 % Allowed : 11.32 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.27), residues: 898 helix: 0.87 (0.26), residues: 398 sheet: -0.40 (0.59), residues: 79 loop : -0.72 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 184 HIS 0.005 0.001 HIS A 936 PHE 0.033 0.002 PHE A 76 TYR 0.026 0.002 TYR A 698 ARG 0.011 0.001 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8071 (mp) REVERT: A 183 GLN cc_start: 0.8260 (mt0) cc_final: 0.7819 (mt0) REVERT: A 217 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: A 554 LEU cc_start: 0.0252 (OUTLIER) cc_final: 0.0046 (mt) REVERT: A 805 GLU cc_start: 0.7144 (tp30) cc_final: 0.6535 (tp30) REVERT: A 895 GLU cc_start: 0.6446 (mp0) cc_final: 0.6016 (pm20) outliers start: 23 outliers final: 10 residues processed: 74 average time/residue: 1.7847 time to fit residues: 141.2209 Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1007 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 58 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10176 Z= 0.319 Angle : 0.680 9.302 14366 Z= 0.351 Chirality : 0.043 0.314 1653 Planarity : 0.006 0.050 1420 Dihedral : 22.189 160.813 2766 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.10 % Allowed : 11.86 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.27), residues: 898 helix: 0.95 (0.26), residues: 398 sheet: -0.40 (0.60), residues: 79 loop : -0.68 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 184 HIS 0.004 0.001 HIS A 486 PHE 0.032 0.002 PHE A 76 TYR 0.027 0.002 TYR A 698 ARG 0.015 0.001 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8240 (mt0) cc_final: 0.7808 (mt0) REVERT: A 217 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: A 805 GLU cc_start: 0.7132 (tp30) cc_final: 0.6529 (tp30) REVERT: A 895 GLU cc_start: 0.6449 (mp0) cc_final: 0.6021 (pm20) outliers start: 23 outliers final: 12 residues processed: 70 average time/residue: 1.6605 time to fit residues: 123.5399 Evaluate side-chains 63 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1007 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10176 Z= 0.167 Angle : 0.560 8.044 14366 Z= 0.295 Chirality : 0.038 0.277 1653 Planarity : 0.004 0.046 1420 Dihedral : 21.970 163.199 2766 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.81 % Allowed : 14.15 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 898 helix: 1.34 (0.26), residues: 397 sheet: -0.28 (0.61), residues: 79 loop : -0.50 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 161 HIS 0.005 0.001 HIS A 486 PHE 0.026 0.002 PHE A 76 TYR 0.020 0.001 TYR A 698 ARG 0.011 0.000 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8141 (mt0) cc_final: 0.7735 (mt0) REVERT: A 805 GLU cc_start: 0.7121 (tp30) cc_final: 0.6545 (tp30) REVERT: A 882 LEU cc_start: 0.8106 (tp) cc_final: 0.7865 (tp) REVERT: A 895 GLU cc_start: 0.6215 (mp0) cc_final: 0.5846 (pm20) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 1.5956 time to fit residues: 105.4822 Evaluate side-chains 57 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 486 HIS A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10176 Z= 0.421 Angle : 0.756 8.908 14366 Z= 0.385 Chirality : 0.046 0.325 1653 Planarity : 0.006 0.063 1420 Dihedral : 22.177 159.425 2766 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.89 % Allowed : 13.48 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 898 helix: 0.92 (0.26), residues: 398 sheet: -0.40 (0.59), residues: 79 loop : -0.66 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 854 HIS 0.006 0.002 HIS A 936 PHE 0.033 0.003 PHE A 76 TYR 0.033 0.003 TYR A 698 ARG 0.020 0.001 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7545 (mpt180) REVERT: A 183 GLN cc_start: 0.8307 (mt0) cc_final: 0.7871 (mt0) REVERT: A 217 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: A 554 LEU cc_start: 0.0337 (OUTLIER) cc_final: 0.0119 (mt) REVERT: A 805 GLU cc_start: 0.7134 (tp30) cc_final: 0.6525 (tp30) REVERT: A 895 GLU cc_start: 0.6565 (mp0) cc_final: 0.6080 (pm20) outliers start: 14 outliers final: 7 residues processed: 65 average time/residue: 1.6225 time to fit residues: 112.2843 Evaluate side-chains 61 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1007 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10176 Z= 0.224 Angle : 0.605 7.856 14366 Z= 0.316 Chirality : 0.040 0.290 1653 Planarity : 0.005 0.047 1420 Dihedral : 22.024 162.490 2766 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.21 % Allowed : 14.15 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.28), residues: 898 helix: 1.22 (0.26), residues: 397 sheet: -0.37 (0.60), residues: 79 loop : -0.56 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.005 0.001 HIS A 486 PHE 0.031 0.002 PHE A 76 TYR 0.027 0.002 TYR A 698 ARG 0.016 0.001 ARG A1048 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8207 (mt0) cc_final: 0.7810 (mt0) REVERT: A 217 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: A 554 LEU cc_start: 0.0422 (OUTLIER) cc_final: 0.0204 (mt) REVERT: A 805 GLU cc_start: 0.7154 (tp30) cc_final: 0.6611 (tp30) REVERT: A 882 LEU cc_start: 0.8109 (tp) cc_final: 0.7819 (tp) REVERT: A 895 GLU cc_start: 0.6379 (mp0) cc_final: 0.5947 (pm20) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 1.5696 time to fit residues: 106.8596 Evaluate side-chains 58 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.202138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151154 restraints weight = 9468.893| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.07 r_work: 0.3315 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10176 Z= 0.245 Angle : 0.614 7.742 14366 Z= 0.319 Chirality : 0.040 0.293 1653 Planarity : 0.005 0.048 1420 Dihedral : 21.973 162.200 2766 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.48 % Allowed : 13.88 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.28), residues: 898 helix: 1.26 (0.26), residues: 397 sheet: -0.37 (0.60), residues: 79 loop : -0.56 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.005 0.001 HIS A 486 PHE 0.030 0.002 PHE A 76 TYR 0.026 0.002 TYR A 698 ARG 0.018 0.001 ARG A1048 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2757.09 seconds wall clock time: 50 minutes 31.86 seconds (3031.86 seconds total)