Starting phenix.real_space_refine on Thu Mar 14 20:30:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2q_27146/03_2024/8d2q_27146.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2q_27146/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2q_27146/03_2024/8d2q_27146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2q_27146/03_2024/8d2q_27146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2q_27146/03_2024/8d2q_27146.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2q_27146/03_2024/8d2q_27146.pdb" } 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 Residue "A ASP 234": "OD1" <-> "OD2" Residue "A GLU 805": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.17, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 4.20 Conformation dependent library (CDL) restraints added in 1.4 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: 4.12 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: 5.16 Time building geometry restraints manager: 4.54 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: 89.19 - 98.55: 6 98.55 - 107.90: 1409 107.90 - 117.26: 6506 117.26 - 126.62: 5955 126.62 - 135.98: 490 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 2.440 nonbonded pdb=" OG1 THR A 684 " pdb=" OP1 DT T 23 " model vdw 2.256 2.440 ... (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 ========== 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: 1.420 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: 6.560 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.630 Find NCS groups from input model: 0.230 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.570 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.892 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: 1.6816 time to fit residues: 128.0342 Evaluate side-chains 57 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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: 0.8980 chunk 42 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 0.0370 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10176 Z= 0.170 Angle : 0.571 7.968 14366 Z= 0.299 Chirality : 0.037 0.233 1653 Planarity : 0.005 0.042 1420 Dihedral : 22.065 155.037 2766 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 5.80 % Favored : 93.53 % 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: -0.30 (0.26), residues: 898 helix: 0.56 (0.26), residues: 396 sheet: -0.14 (0.53), residues: 83 loop : -0.90 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.005 0.001 HIS A 749 PHE 0.023 0.001 PHE A 76 TYR 0.010 0.001 TYR A 986 ARG 0.009 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 68 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.845 Fit side-chains REVERT: A 576 MET cc_start: 0.1506 (OUTLIER) cc_final: 0.1109 (mmt) REVERT: A 802 GLN cc_start: 0.6920 (tp40) cc_final: 0.6417 (tt0) REVERT: A 805 GLU cc_start: 0.7128 (tp30) cc_final: 0.6538 (tp30) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 1.4854 time to fit residues: 102.9363 Evaluate side-chains 60 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 28 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1555 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 : 0.702 8.684 14366 Z= 0.361 Chirality : 0.044 0.264 1653 Planarity : 0.006 0.048 1420 Dihedral : 22.196 155.232 2766 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.75 % Allowed : 7.68 % Favored : 90.57 % 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 (0.26), residues: 898 helix: 0.84 (0.26), residues: 396 sheet: -0.43 (0.53), residues: 84 loop : -0.85 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 145 HIS 0.006 0.001 HIS A 486 PHE 0.029 0.002 PHE A 76 TYR 0.018 0.002 TYR A 986 ARG 0.009 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 74 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8263 (mt0) cc_final: 0.7842 (mt0) REVERT: A 230 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.5801 (mpt90) REVERT: A 805 GLU cc_start: 0.7202 (tp30) cc_final: 0.6599 (tp30) REVERT: A 894 ASP cc_start: 0.6254 (t0) cc_final: 0.5936 (t0) outliers start: 13 outliers final: 6 residues processed: 70 average time/residue: 1.6165 time to fit residues: 120.4446 Evaluate side-chains 65 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 678 ILE 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: 7.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10176 Z= 0.217 Angle : 0.584 8.056 14366 Z= 0.305 Chirality : 0.039 0.241 1653 Planarity : 0.005 0.042 1420 Dihedral : 22.091 156.070 2766 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.62 % Allowed : 9.84 % Favored : 88.54 % 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: 0.18 (0.27), residues: 898 helix: 1.13 (0.26), residues: 397 sheet: -0.47 (0.53), residues: 84 loop : -0.71 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.004 0.001 HIS A 486 PHE 0.027 0.002 PHE A 76 TYR 0.013 0.001 TYR A 986 ARG 0.010 0.001 ARG A1048 *********************** 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 71 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8209 (mt0) cc_final: 0.7815 (mt0) REVERT: A 230 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.5846 (mpt90) REVERT: A 805 GLU cc_start: 0.7125 (tp30) cc_final: 0.6546 (tp30) REVERT: A 894 ASP cc_start: 0.6177 (t0) cc_final: 0.5905 (t0) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 1.4760 time to fit residues: 105.5409 Evaluate side-chains 63 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 678 ILE 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: 2.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 649 ASN A 802 GLN A 946 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1850 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= 0.310 Angle : 0.655 7.625 14366 Z= 0.338 Chirality : 0.042 0.254 1653 Planarity : 0.006 0.047 1420 Dihedral : 22.145 156.039 2766 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.02 % Allowed : 10.78 % Favored : 87.20 % 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: 0.10 (0.27), residues: 898 helix: 1.05 (0.26), residues: 397 sheet: -0.49 (0.54), residues: 84 loop : -0.73 (0.28), residues: 417 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 0.028 0.002 PHE A 76 TYR 0.017 0.002 TYR A 986 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 72 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8257 (mt0) cc_final: 0.7824 (mt0) REVERT: A 230 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.5833 (mpt90) REVERT: A 802 GLN cc_start: 0.6859 (tp-100) cc_final: 0.6656 (tt0) REVERT: A 805 GLU cc_start: 0.7144 (tp30) cc_final: 0.6551 (tp30) REVERT: A 882 LEU cc_start: 0.8132 (tp) cc_final: 0.7881 (tp) REVERT: A 894 ASP cc_start: 0.6188 (t0) cc_final: 0.5950 (t0) outliers start: 15 outliers final: 7 residues processed: 68 average time/residue: 1.4884 time to fit residues: 107.6980 Evaluate side-chains 64 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 484 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.7302 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.1881 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= 0.231 Angle : 0.597 7.551 14366 Z= 0.311 Chirality : 0.039 0.240 1653 Planarity : 0.005 0.044 1420 Dihedral : 22.044 156.559 2766 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.16 % Allowed : 11.46 % Favored : 86.39 % 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: 0.26 (0.27), residues: 898 helix: 1.25 (0.26), residues: 398 sheet: -0.50 (0.55), residues: 84 loop : -0.70 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.004 0.001 HIS A 486 PHE 0.028 0.002 PHE A 76 TYR 0.015 0.002 TYR A 698 ARG 0.013 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 71 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8222 (mt0) cc_final: 0.7801 (mt0) REVERT: A 230 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.5814 (mpt90) REVERT: A 802 GLN cc_start: 0.6875 (tp-100) cc_final: 0.6671 (tt0) REVERT: A 805 GLU cc_start: 0.7136 (tp30) cc_final: 0.6545 (tp30) REVERT: A 882 LEU cc_start: 0.8126 (tp) cc_final: 0.7836 (tp) outliers start: 16 outliers final: 8 residues processed: 67 average time/residue: 1.5407 time to fit residues: 110.0582 Evaluate side-chains 62 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS 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: 0.7980 chunk 55 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 946 HIS A1060 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10176 Z= 0.272 Angle : 0.627 7.272 14366 Z= 0.325 Chirality : 0.041 0.246 1653 Planarity : 0.005 0.044 1420 Dihedral : 22.035 156.486 2766 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.75 % Allowed : 12.26 % Favored : 85.98 % 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: 0.23 (0.27), residues: 898 helix: 1.22 (0.26), residues: 398 sheet: -0.54 (0.55), residues: 84 loop : -0.71 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.004 0.001 HIS A 936 PHE 0.028 0.002 PHE A 76 TYR 0.016 0.002 TYR A 986 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 67 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8229 (mt0) cc_final: 0.7799 (mt0) REVERT: A 230 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.5806 (mpt90) REVERT: A 802 GLN cc_start: 0.6903 (tp-100) cc_final: 0.6699 (tt0) REVERT: A 805 GLU cc_start: 0.7126 (tp30) cc_final: 0.6535 (tp30) REVERT: A 895 GLU cc_start: 0.6444 (mp0) cc_final: 0.5908 (pm20) outliers start: 13 outliers final: 10 residues processed: 64 average time/residue: 1.5196 time to fit residues: 103.2900 Evaluate side-chains 65 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 678 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: 7.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.0070 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2014 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= 0.222 Angle : 0.581 6.910 14366 Z= 0.304 Chirality : 0.039 0.235 1653 Planarity : 0.005 0.044 1420 Dihedral : 21.933 156.894 2766 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.48 % Allowed : 12.94 % 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: 0.39 (0.27), residues: 898 helix: 1.40 (0.26), residues: 397 sheet: -0.51 (0.55), residues: 84 loop : -0.66 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.003 0.001 HIS A 486 PHE 0.027 0.002 PHE A 76 TYR 0.015 0.001 TYR A 698 ARG 0.013 0.001 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 67 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8216 (mt0) cc_final: 0.7815 (mt0) REVERT: A 230 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.5830 (mpt90) REVERT: A 805 GLU cc_start: 0.7126 (tp30) cc_final: 0.6535 (tp30) REVERT: A 882 LEU cc_start: 0.8099 (tp) cc_final: 0.7805 (tp) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 1.4511 time to fit residues: 99.0196 Evaluate side-chains 64 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 484 THR 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 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=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: 9.9990 chunk 39 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 95 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10176 Z= 0.288 Angle : 0.635 7.333 14366 Z= 0.329 Chirality : 0.041 0.246 1653 Planarity : 0.005 0.044 1420 Dihedral : 21.970 156.546 2766 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.29 % Allowed : 12.26 % Favored : 85.44 % 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: 0.27 (0.27), residues: 898 helix: 1.26 (0.26), residues: 398 sheet: -0.55 (0.55), residues: 84 loop : -0.68 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 145 HIS 0.004 0.001 HIS A 486 PHE 0.030 0.002 PHE A 76 TYR 0.021 0.002 TYR A 698 ARG 0.017 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 70 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8235 (mt0) cc_final: 0.7803 (mt0) REVERT: A 217 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: A 230 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.5805 (mpt90) REVERT: A 554 LEU cc_start: 0.0170 (OUTLIER) cc_final: -0.0030 (mt) REVERT: A 805 GLU cc_start: 0.7112 (tp30) cc_final: 0.6517 (tp30) REVERT: A 894 ASP cc_start: 0.6455 (t0) cc_final: 0.6195 (t0) outliers start: 17 outliers final: 10 residues processed: 67 average time/residue: 1.5533 time to fit residues: 110.6988 Evaluate side-chains 66 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 230 ARG Chi-restraints excluded: chain A residue 484 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10176 Z= 0.167 Angle : 0.547 6.824 14366 Z= 0.288 Chirality : 0.037 0.222 1653 Planarity : 0.005 0.098 1420 Dihedral : 21.826 156.900 2766 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.94 % Allowed : 13.48 % 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: 0.57 (0.28), residues: 898 helix: 1.56 (0.26), residues: 397 sheet: -0.45 (0.56), residues: 84 loop : -0.56 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.003 0.001 HIS A 486 PHE 0.026 0.001 PHE A 76 TYR 0.017 0.001 TYR A 698 ARG 0.011 0.000 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 63 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8174 (mt0) cc_final: 0.7778 (mt0) REVERT: A 217 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: A 230 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.5826 (mpt90) REVERT: A 805 GLU cc_start: 0.7042 (tp30) cc_final: 0.6466 (tp30) REVERT: A 882 LEU cc_start: 0.8106 (tp) cc_final: 0.7827 (tp) REVERT: A 894 ASP cc_start: 0.6419 (t0) cc_final: 0.6102 (t0) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 1.5921 time to fit residues: 107.6124 Evaluate side-chains 60 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 VAL 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: 0.6980 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.203307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158483 restraints weight = 9500.392| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.76 r_work: 0.3333 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10176 Z= 0.228 Angle : 0.582 6.541 14366 Z= 0.303 Chirality : 0.039 0.231 1653 Planarity : 0.004 0.043 1420 Dihedral : 21.809 156.372 2766 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.21 % Allowed : 13.34 % Favored : 85.44 % 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: 0.49 (0.27), residues: 898 helix: 1.47 (0.26), residues: 397 sheet: -0.51 (0.56), residues: 84 loop : -0.57 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.004 0.001 HIS A 486 PHE 0.026 0.002 PHE A1086 TYR 0.016 0.002 TYR A 698 ARG 0.013 0.001 ARG A1048 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.85 seconds wall clock time: 49 minutes 24.08 seconds (2964.08 seconds total)