Starting phenix.real_space_refine on Thu Feb 15 12:42:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/02_2024/8d2k_27141_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/02_2024/8d2k_27141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/02_2024/8d2k_27141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/02_2024/8d2k_27141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/02_2024/8d2k_27141_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/02_2024/8d2k_27141_updated.pdb" } resolution = 2.43 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= 0.007 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 156 5.49 5 Mg 10 5.21 5 S 20 5.16 5 C 6940 2.51 5 N 2220 2.21 5 O 2949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ASP 812": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12295 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8720 Classifications: {'peptide': 1105} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Chain: "B" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2189 Unusual residues: {'GTP': 1} Classifications: {'RNA': 101, 'undetermined': 1} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 47, 'rna3p_pyr': 41} Link IDs: {'rna2p': 13, 'rna3p': 87, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 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: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 12} Chain: "Y" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.50, per 1000 atoms: 0.61 Number of scatterers: 12295 At special positions: 0 Unit cell: (94.05, 106.425, 129.525, 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 20 16.00 P 156 15.00 Mg 10 11.99 O 2949 8.00 N 2220 7.00 C 6940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.52 Conformation dependent library (CDL) restraints added in 1.7 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 7 sheets defined 43.3% alpha, 8.7% beta 55 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 6.59 Creating SS restraints... Processing helix chain 'A' and resid 60 through 91 Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 121 through 137 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 240 through 250 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 393 through 405 Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 442 through 455 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 487 through 507 Processing helix chain 'A' and resid 525 through 552 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 634 through 642 Processing helix chain 'A' and resid 654 through 668 Processing helix chain 'A' and resid 682 through 702 Processing helix chain 'A' and resid 712 through 721 Processing helix chain 'A' and resid 726 through 729 No H-bonds generated for 'chain 'A' and resid 726 through 729' Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 747 through 759 removed outlier: 3.676A pdb=" N HIS A 750 " --> pdb=" O ARG A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 776 Processing helix chain 'A' and resid 798 through 806 Processing helix chain 'A' and resid 810 through 819 Processing helix chain 'A' and resid 856 through 860 Processing helix chain 'A' and resid 865 through 875 Processing helix chain 'A' and resid 957 through 962 Processing helix chain 'A' and resid 982 through 985 No H-bonds generated for 'chain 'A' and resid 982 through 985' Processing helix chain 'A' and resid 989 through 997 Processing helix chain 'A' and resid 1026 through 1032 removed outlier: 4.140A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1070 removed outlier: 3.833A pdb=" N SER A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A1070 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1085 Processing helix chain 'A' and resid 1094 through 1097 No H-bonds generated for 'chain 'A' and resid 1094 through 1097' Processing sheet with id= A, first strand: chain 'A' and resid 706 through 711 removed outlier: 3.759A pdb=" N SER A 512 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL A 19 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER A 30 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE A 39 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA A 824 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE A 46 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A 826 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 295 through 298 Processing sheet with id= C, first strand: chain 'A' and resid 588 through 591 Processing sheet with id= D, first strand: chain 'A' and resid 846 through 849 Processing sheet with id= E, first strand: chain 'A' and resid 921 through 924 Processing sheet with id= F, first strand: chain 'A' and resid 1104 through 1106 removed outlier: 3.719A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 949 through 956 removed outlier: 3.587A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 7.81 Time building geometry restraints manager: 6.83 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: 2214 1.33 - 1.45: 3804 1.45 - 1.57: 6203 1.57 - 1.69: 306 1.69 - 1.81: 28 Bond restraints: 12555 Sorted by residual: bond pdb=" C3' G B 97 " pdb=" O3' G B 97 " ideal model delta sigma weight residual 1.427 1.480 -0.053 1.50e-02 4.44e+03 1.25e+01 bond pdb=" C3' DA D 29 " pdb=" O3' DA D 29 " ideal model delta sigma weight residual 1.422 1.517 -0.095 3.00e-02 1.11e+03 1.01e+01 bond pdb=" O3' G B 97 " pdb=" P A B 98 " ideal model delta sigma weight residual 1.607 1.650 -0.043 1.50e-02 4.44e+03 8.35e+00 bond pdb=" C3' DA X 1 " pdb=" O3' DA X 1 " ideal model delta sigma weight residual 1.422 1.502 -0.080 3.00e-02 1.11e+03 7.18e+00 bond pdb=" CB TRP A1128 " pdb=" CG TRP A1128 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.16e+00 ... (remaining 12550 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.10: 1088 106.10 - 113.16: 6822 113.16 - 120.22: 4773 120.22 - 127.28: 4623 127.28 - 134.34: 441 Bond angle restraints: 17747 Sorted by residual: angle pdb=" C3' G B 97 " pdb=" O3' G B 97 " pdb=" P A B 98 " ideal model delta sigma weight residual 120.20 132.67 -12.47 1.50e+00 4.44e-01 6.91e+01 angle pdb=" C3' DA D 29 " pdb=" O3' DA D 29 " pdb=" P DT D 30 " ideal model delta sigma weight residual 120.20 127.99 -7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" N GLU A 548 " pdb=" CA GLU A 548 " pdb=" CB GLU A 548 " ideal model delta sigma weight residual 110.28 118.15 -7.87 1.55e+00 4.16e-01 2.58e+01 angle pdb=" C3' C B 96 " pdb=" O3' C B 96 " pdb=" P G B 97 " ideal model delta sigma weight residual 120.20 127.44 -7.24 1.50e+00 4.44e-01 2.33e+01 angle pdb=" O3' G B 97 " pdb=" C3' G B 97 " pdb=" C2' G B 97 " ideal model delta sigma weight residual 109.50 116.42 -6.92 1.50e+00 4.44e-01 2.13e+01 ... (remaining 17742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 7052 34.86 - 69.71: 493 69.71 - 104.57: 46 104.57 - 139.42: 2 139.42 - 174.28: 2 Dihedral angle restraints: 7595 sinusoidal: 4399 harmonic: 3196 Sorted by residual: dihedral pdb=" O4' A B 98 " pdb=" C2' A B 98 " pdb=" C1' A B 98 " pdb=" C3' A B 98 " ideal model delta sinusoidal sigma weight residual 25.00 -13.57 38.57 1 8.00e+00 1.56e-02 3.27e+01 dihedral pdb=" C4' A B 98 " pdb=" O4' A B 98 " pdb=" C1' A B 98 " pdb=" C2' A B 98 " ideal model delta sinusoidal sigma weight residual 3.00 -30.59 33.59 1 8.00e+00 1.56e-02 2.50e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 18.39 86.20 1 2.00e+01 2.50e-03 2.24e+01 ... (remaining 7592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1960 0.112 - 0.225: 77 0.225 - 0.337: 7 0.337 - 0.449: 0 0.449 - 0.562: 1 Chirality restraints: 2045 Sorted by residual: chirality pdb=" CG LEU A1075 " pdb=" CB LEU A1075 " pdb=" CD1 LEU A1075 " pdb=" CD2 LEU A1075 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" CG LEU A 399 " pdb=" CB LEU A 399 " pdb=" CD1 LEU A 399 " pdb=" CD2 LEU A 399 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE A 681 " pdb=" CA ILE A 681 " pdb=" CG1 ILE A 681 " pdb=" CG2 ILE A 681 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 2042 not shown) Planarity restraints: 1743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1128 " -0.021 2.00e-02 2.50e+03 3.62e-02 3.27e+01 pdb=" CG TRP A1128 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP A1128 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP A1128 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A1128 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A1128 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1128 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1128 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1128 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A1128 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 97 " -0.020 2.00e-02 2.50e+03 3.05e-02 2.78e+01 pdb=" N9 G B 97 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B 97 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 97 " 0.013 2.00e-02 2.50e+03 pdb=" C5 G B 97 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 97 " 0.056 2.00e-02 2.50e+03 pdb=" O6 G B 97 " -0.054 2.00e-02 2.50e+03 pdb=" N1 G B 97 " -0.013 2.00e-02 2.50e+03 pdb=" C2 G B 97 " 0.041 2.00e-02 2.50e+03 pdb=" N2 G B 97 " -0.034 2.00e-02 2.50e+03 pdb=" N3 G B 97 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G B 97 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 88 " 0.044 2.00e-02 2.50e+03 3.33e-02 2.50e+01 pdb=" N1 C B 88 " -0.072 2.00e-02 2.50e+03 pdb=" C2 C B 88 " 0.035 2.00e-02 2.50e+03 pdb=" O2 C B 88 " -0.011 2.00e-02 2.50e+03 pdb=" N3 C B 88 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C B 88 " -0.028 2.00e-02 2.50e+03 pdb=" N4 C B 88 " 0.025 2.00e-02 2.50e+03 pdb=" C5 C B 88 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C B 88 " -0.001 2.00e-02 2.50e+03 ... (remaining 1740 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 244 2.58 - 3.16: 9375 3.16 - 3.74: 23732 3.74 - 4.32: 32185 4.32 - 4.90: 47096 Nonbonded interactions: 112632 Sorted by model distance: nonbonded pdb=" OD2 ASP A 18 " pdb="MG MG A1203 " model vdw 2.000 2.170 nonbonded pdb=" OP1 U B 78 " pdb="MG MG B 204 " model vdw 2.002 2.170 nonbonded pdb=" OP2 DC T 14 " pdb="MG MG A1201 " model vdw 2.015 2.170 nonbonded pdb=" OP3 DT D 28 " pdb="MG MG A1203 " model vdw 2.025 2.170 nonbonded pdb=" OP2 DT D 28 " pdb="MG MG A1202 " model vdw 2.030 2.170 ... (remaining 112627 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 6.890 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 46.030 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 0.095 12555 Z= 0.386 Angle : 0.908 12.468 17747 Z= 0.481 Chirality : 0.054 0.562 2045 Planarity : 0.008 0.081 1743 Dihedral : 20.179 174.276 5521 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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 (0.23), residues: 1097 helix: 0.16 (0.21), residues: 539 sheet: -0.31 (0.56), residues: 82 loop : -0.24 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP A1128 HIS 0.007 0.002 HIS A 946 PHE 0.072 0.004 PHE A 363 TYR 0.019 0.003 TYR A 986 ARG 0.017 0.001 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.111 Fit side-chains REVERT: A 311 ASN cc_start: 0.7667 (m-40) cc_final: 0.7338 (m-40) REVERT: A 358 SER cc_start: 0.7626 (m) cc_final: 0.7420 (m) REVERT: A 720 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.6494 (ttp-170) REVERT: A 723 ASP cc_start: 0.5636 (m-30) cc_final: 0.5329 (m-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 1.9244 time to fit residues: 236.7260 Evaluate side-chains 90 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0570 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 377 ASN A1084 GLN A1113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12555 Z= 0.232 Angle : 0.588 8.734 17747 Z= 0.308 Chirality : 0.039 0.314 2045 Planarity : 0.005 0.060 1743 Dihedral : 21.402 176.358 3432 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.20 % Allowed : 6.67 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.67 (0.24), residues: 1097 helix: 1.00 (0.22), residues: 540 sheet: -0.45 (0.55), residues: 83 loop : 0.12 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1128 HIS 0.008 0.001 HIS A 603 PHE 0.021 0.002 PHE A 282 TYR 0.015 0.002 TYR A 986 ARG 0.006 0.001 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.121 Fit side-chains REVERT: A 311 ASN cc_start: 0.7626 (m-40) cc_final: 0.7191 (m-40) REVERT: A 548 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5658 (mp0) REVERT: A 602 ARG cc_start: 0.7606 (mtp85) cc_final: 0.7341 (mtm-85) REVERT: A 723 ASP cc_start: 0.5602 (m-30) cc_final: 0.5343 (m-30) REVERT: A 724 ILE cc_start: 0.7465 (mm) cc_final: 0.7154 (mt) REVERT: A 1025 ASP cc_start: 0.6374 (t0) cc_final: 0.6107 (t70) outliers start: 11 outliers final: 4 residues processed: 102 average time/residue: 1.8708 time to fit residues: 203.1408 Evaluate side-chains 94 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 377 ASN A1113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 12555 Z= 0.466 Angle : 0.747 9.455 17747 Z= 0.389 Chirality : 0.048 0.249 2045 Planarity : 0.007 0.065 1743 Dihedral : 21.557 178.208 3432 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.75 % Allowed : 7.98 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.46 (0.24), residues: 1097 helix: 0.75 (0.22), residues: 543 sheet: -0.40 (0.53), residues: 88 loop : 0.08 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 13 HIS 0.008 0.002 HIS A 603 PHE 0.024 0.003 PHE A 282 TYR 0.023 0.003 TYR A 986 ARG 0.011 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7579 (m-40) cc_final: 0.7142 (m-40) REVERT: A 662 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7322 (mtpt) REVERT: A 720 ARG cc_start: 0.6986 (ttp-170) cc_final: 0.6425 (ttp-170) REVERT: A 747 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7322 (mtp85) outliers start: 16 outliers final: 7 residues processed: 99 average time/residue: 2.0334 time to fit residues: 214.0924 Evaluate side-chains 93 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12555 Z= 0.309 Angle : 0.636 9.514 17747 Z= 0.332 Chirality : 0.042 0.230 2045 Planarity : 0.005 0.053 1743 Dihedral : 21.443 175.914 3432 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.75 % Allowed : 8.96 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.68 (0.24), residues: 1097 helix: 0.98 (0.22), residues: 538 sheet: -0.41 (0.57), residues: 77 loop : 0.16 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 749 PHE 0.021 0.002 PHE A 282 TYR 0.019 0.002 TYR A 986 ARG 0.005 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7570 (m-40) cc_final: 0.7124 (m-40) REVERT: A 602 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7506 (mtt-85) REVERT: A 662 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7291 (mtpt) REVERT: A 720 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6389 (ttp-170) REVERT: A 747 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7302 (mtp85) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 1.8513 time to fit residues: 187.3599 Evaluate side-chains 91 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 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 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12555 Z= 0.238 Angle : 0.587 9.434 17747 Z= 0.307 Chirality : 0.039 0.222 2045 Planarity : 0.005 0.051 1743 Dihedral : 21.362 175.122 3432 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.53 % Allowed : 9.95 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.93 (0.25), residues: 1097 helix: 1.22 (0.22), residues: 536 sheet: -0.43 (0.56), residues: 77 loop : 0.27 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.020 0.002 PHE A 282 TYR 0.017 0.002 TYR A 986 ARG 0.005 0.000 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7547 (m-40) cc_final: 0.7017 (m-40) REVERT: A 377 ASN cc_start: 0.5894 (m-40) cc_final: 0.5643 (m110) REVERT: A 662 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7290 (mtpt) REVERT: A 720 ARG cc_start: 0.6924 (ttp-170) cc_final: 0.6378 (ttp-170) REVERT: A 726 ILE cc_start: 0.6751 (mm) cc_final: 0.6366 (mp) REVERT: A 747 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7082 (mtp85) outliers start: 14 outliers final: 8 residues processed: 97 average time/residue: 1.9196 time to fit residues: 198.1243 Evaluate side-chains 98 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 0.0060 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 overall best weight: 2.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12555 Z= 0.283 Angle : 0.614 9.385 17747 Z= 0.321 Chirality : 0.041 0.224 2045 Planarity : 0.005 0.050 1743 Dihedral : 21.381 175.765 3432 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.75 % Allowed : 11.04 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.91 (0.25), residues: 1097 helix: 1.20 (0.22), residues: 536 sheet: -0.51 (0.55), residues: 76 loop : 0.27 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 749 PHE 0.021 0.002 PHE A 282 TYR 0.019 0.002 TYR A 986 ARG 0.005 0.001 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7582 (m-40) cc_final: 0.7042 (m-40) REVERT: A 630 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6801 (m-40) REVERT: A 662 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7289 (mtpt) REVERT: A 720 ARG cc_start: 0.6927 (ttp-170) cc_final: 0.6389 (ttp-170) REVERT: A 726 ILE cc_start: 0.6771 (mm) cc_final: 0.6397 (mp) outliers start: 16 outliers final: 8 residues processed: 97 average time/residue: 1.8402 time to fit residues: 190.2329 Evaluate side-chains 94 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 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 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12555 Z= 0.301 Angle : 0.626 9.410 17747 Z= 0.327 Chirality : 0.041 0.225 2045 Planarity : 0.005 0.078 1743 Dihedral : 21.410 175.832 3432 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.97 % Allowed : 11.26 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.88 (0.25), residues: 1097 helix: 1.16 (0.22), residues: 537 sheet: -0.49 (0.55), residues: 76 loop : 0.27 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 749 PHE 0.021 0.002 PHE A 282 TYR 0.019 0.002 TYR A 986 ARG 0.009 0.001 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.187 Fit side-chains REVERT: A 137 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.6441 (mtt180) REVERT: A 311 ASN cc_start: 0.7579 (m-40) cc_final: 0.7028 (m-40) REVERT: A 377 ASN cc_start: 0.6121 (m-40) cc_final: 0.5847 (m110) REVERT: A 548 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5358 (mp0) REVERT: A 662 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7293 (mtpt) REVERT: A 720 ARG cc_start: 0.6929 (ttp-170) cc_final: 0.6394 (ttp-170) REVERT: A 726 ILE cc_start: 0.6774 (mm) cc_final: 0.6421 (mp) REVERT: A 1028 MET cc_start: 0.6811 (ptm) cc_final: 0.6359 (tpt) outliers start: 18 outliers final: 9 residues processed: 96 average time/residue: 1.8800 time to fit residues: 192.2462 Evaluate side-chains 94 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 1084 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12555 Z= 0.250 Angle : 0.591 9.448 17747 Z= 0.309 Chirality : 0.039 0.224 2045 Planarity : 0.005 0.051 1743 Dihedral : 21.382 175.209 3432 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.31 % Allowed : 12.57 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.98 (0.25), residues: 1097 helix: 1.26 (0.22), residues: 537 sheet: -0.53 (0.56), residues: 76 loop : 0.32 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 749 PHE 0.020 0.002 PHE A 282 TYR 0.017 0.002 TYR A 986 ARG 0.007 0.000 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.218 Fit side-chains REVERT: A 137 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.6401 (mtt180) REVERT: A 311 ASN cc_start: 0.7588 (m-40) cc_final: 0.7038 (m-40) REVERT: A 548 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5140 (mp0) REVERT: A 726 ILE cc_start: 0.6782 (mm) cc_final: 0.6437 (mp) REVERT: A 1028 MET cc_start: 0.6800 (ptm) cc_final: 0.6362 (tpt) outliers start: 12 outliers final: 10 residues processed: 93 average time/residue: 1.8662 time to fit residues: 184.9546 Evaluate side-chains 95 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 1084 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 0.0370 chunk 100 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12555 Z= 0.219 Angle : 0.577 9.397 17747 Z= 0.301 Chirality : 0.038 0.223 2045 Planarity : 0.005 0.051 1743 Dihedral : 21.369 174.986 3432 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.53 % Allowed : 12.35 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1097 helix: 1.31 (0.22), residues: 537 sheet: -0.57 (0.56), residues: 76 loop : 0.33 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.019 0.002 PHE A 282 TYR 0.017 0.002 TYR A 986 ARG 0.010 0.000 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.295 Fit side-chains REVERT: A 137 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.6371 (mtt180) REVERT: A 311 ASN cc_start: 0.7584 (m-40) cc_final: 0.7031 (m-40) REVERT: A 548 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5140 (mp0) REVERT: A 662 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7288 (mtpt) REVERT: A 726 ILE cc_start: 0.6781 (mm) cc_final: 0.6438 (mp) REVERT: A 1028 MET cc_start: 0.6805 (ptm) cc_final: 0.6369 (tpt) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 1.8847 time to fit residues: 196.5087 Evaluate side-chains 96 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 1084 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12555 Z= 0.235 Angle : 0.584 9.337 17747 Z= 0.305 Chirality : 0.039 0.222 2045 Planarity : 0.005 0.096 1743 Dihedral : 21.341 174.903 3432 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.75 % Allowed : 12.24 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1097 helix: 1.31 (0.22), residues: 537 sheet: -0.56 (0.56), residues: 76 loop : 0.33 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.020 0.002 PHE A 282 TYR 0.017 0.002 TYR A 986 ARG 0.011 0.000 ARG A1048 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 1.302 Fit side-chains REVERT: A 137 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.6393 (mtt180) REVERT: A 311 ASN cc_start: 0.7559 (m-40) cc_final: 0.7000 (m-40) REVERT: A 377 ASN cc_start: 0.6119 (m-40) cc_final: 0.5783 (m110) REVERT: A 548 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5052 (mp0) REVERT: A 662 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7283 (mtpt) REVERT: A 726 ILE cc_start: 0.6787 (mm) cc_final: 0.6430 (mp) REVERT: A 1028 MET cc_start: 0.6807 (ptm) cc_final: 0.6354 (tpt) outliers start: 16 outliers final: 10 residues processed: 96 average time/residue: 1.8286 time to fit residues: 187.0948 Evaluate side-chains 96 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 1084 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 14 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126808 restraints weight = 10973.187| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.19 r_work: 0.3131 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12555 Z= 0.299 Angle : 0.623 9.297 17747 Z= 0.324 Chirality : 0.041 0.224 2045 Planarity : 0.006 0.121 1743 Dihedral : 21.394 175.722 3432 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.75 % Allowed : 12.24 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.91 (0.25), residues: 1097 helix: 1.20 (0.22), residues: 541 sheet: -0.52 (0.56), residues: 76 loop : 0.27 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 749 PHE 0.021 0.002 PHE A 282 TYR 0.019 0.002 TYR A 986 ARG 0.014 0.001 ARG A1048 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4165.86 seconds wall clock time: 75 minutes 11.70 seconds (4511.70 seconds total)