Starting phenix.real_space_refine on Sat Jul 20 03:23:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewg_28645/07_2024/8ewg_28645.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewg_28645/07_2024/8ewg_28645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewg_28645/07_2024/8ewg_28645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewg_28645/07_2024/8ewg_28645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewg_28645/07_2024/8ewg_28645.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewg_28645/07_2024/8ewg_28645.cif" } resolution = 2.9 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: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 36 5.16 5 C 5861 2.51 5 N 1720 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 877": "OE1" <-> "OE2" Residue "A GLU 885": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9616 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 8423 Classifications: {'peptide': 1017} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 990} Chain breaks: 4 Chain: "B" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1193 Inner-chain residues flagged as termini: ['pdbres=" A B 52 "'] Classifications: {'RNA': 56} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 34} Time building chain proxies: 6.22, per 1000 atoms: 0.65 Number of scatterers: 9616 At special positions: 0 Unit cell: (79.05, 102, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 55 15.00 O 1944 8.00 N 1720 7.00 C 5861 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=0, symmetry=0 Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 1.5 seconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 68.8% alpha, 1.7% beta 8 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.661A pdb=" N ALA A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.560A pdb=" N GLY A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 249 through 272 Processing helix chain 'A' and resid 275 through 294 removed outlier: 4.162A pdb=" N TYR A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 321 through 347 removed outlier: 3.510A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 394 Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.740A pdb=" N ASP A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 453 Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.999A pdb=" N ILE A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 475 through 497 Processing helix chain 'A' and resid 505 through 517 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 535 through 548 removed outlier: 4.030A pdb=" N ALA A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.623A pdb=" N TYR A 553 " --> pdb=" O PRO A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 581 through 607 removed outlier: 3.619A pdb=" N VAL A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 674 removed outlier: 3.545A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 683 through 700 removed outlier: 3.506A pdb=" N THR A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 689 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.704A pdb=" N GLU A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A 721 " --> pdb=" O ILE A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 749 Processing helix chain 'A' and resid 754 through 777 removed outlier: 3.643A pdb=" N ARG A 758 " --> pdb=" O ASP A 754 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.827A pdb=" N ALA A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 827 Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 831 through 850 Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 892 through 899 removed outlier: 5.892A pdb=" N ASP A 897 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 898 " --> pdb=" O PHE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.578A pdb=" N GLU A 907 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 930 removed outlier: 3.708A pdb=" N SER A 930 " --> pdb=" O ARG A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 940 Processing helix chain 'A' and resid 948 through 955 Processing helix chain 'A' and resid 971 through 989 Processing helix chain 'A' and resid 994 through 1019 removed outlier: 3.742A pdb=" N GLU A1002 " --> pdb=" O CYS A 998 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1034 Processing helix chain 'A' and resid 1036 through 1058 Processing helix chain 'A' and resid 1065 through 1073 removed outlier: 3.649A pdb=" N PHE A1073 " --> pdb=" O VAL A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1086 Processing helix chain 'A' and resid 1088 through 1096 removed outlier: 3.563A pdb=" N ASN A1092 " --> pdb=" O GLY A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1116 removed outlier: 4.086A pdb=" N ASN A1112 " --> pdb=" O LEU A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1125 removed outlier: 5.939A pdb=" N LYS A1122 " --> pdb=" O LEU A1119 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN A1123 " --> pdb=" O MET A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1148 Processing helix chain 'A' and resid 1150 through 1167 removed outlier: 4.536A pdb=" N THR A1158 " --> pdb=" O MET A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1221 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA3, first strand: chain 'A' and resid 1173 through 1176 removed outlier: 6.703A pdb=" N ARG A1173 " --> pdb=" O GLU A1185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1191 through 1193 476 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 4.61 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: 2026 1.33 - 1.45: 2513 1.45 - 1.58: 5203 1.58 - 1.70: 109 1.70 - 1.82: 59 Bond restraints: 9910 Sorted by residual: bond pdb=" CA ARG A 992 " pdb=" CB ARG A 992 " ideal model delta sigma weight residual 1.526 1.572 -0.046 1.53e-02 4.27e+03 8.88e+00 bond pdb=" C PHE A1099 " pdb=" N PRO A1100 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.26e+00 bond pdb=" O5' C B 47 " pdb=" C5' C B 47 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.33e+00 bond pdb=" CA VAL A1221 " pdb=" CB VAL A1221 " ideal model delta sigma weight residual 1.531 1.551 -0.020 1.11e-02 8.12e+03 3.12e+00 bond pdb=" C TYR A1222 " pdb=" N PRO A1223 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.45e+00 ... (remaining 9905 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.16: 516 107.16 - 113.95: 5499 113.95 - 120.75: 4454 120.75 - 127.55: 2940 127.55 - 134.34: 183 Bond angle restraints: 13592 Sorted by residual: angle pdb=" CA THR A 802 " pdb=" CB THR A 802 " pdb=" CG2 THR A 802 " ideal model delta sigma weight residual 110.50 117.42 -6.92 1.70e+00 3.46e-01 1.66e+01 angle pdb=" C PHE A 909 " pdb=" N TYR A 910 " pdb=" CA TYR A 910 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" N SER A 362 " pdb=" CA SER A 362 " pdb=" C SER A 362 " ideal model delta sigma weight residual 111.28 115.49 -4.21 1.09e+00 8.42e-01 1.49e+01 angle pdb=" CB MET A1048 " pdb=" CG MET A1048 " pdb=" SD MET A1048 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C4' U B 18 " pdb=" C3' U B 18 " pdb=" O3' U B 18 " ideal model delta sigma weight residual 109.40 114.86 -5.46 1.50e+00 4.44e-01 1.32e+01 ... (remaining 13587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 5708 35.69 - 71.38: 383 71.38 - 107.07: 46 107.07 - 142.76: 1 142.76 - 178.45: 6 Dihedral angle restraints: 6144 sinusoidal: 3148 harmonic: 2996 Sorted by residual: dihedral pdb=" O4' C B 47 " pdb=" C1' C B 47 " pdb=" N1 C B 47 " pdb=" C2 C B 47 " ideal model delta sinusoidal sigma weight residual 200.00 46.21 153.79 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' U B 48 " pdb=" C1' U B 48 " pdb=" N1 U B 48 " pdb=" C2 U B 48 " ideal model delta sinusoidal sigma weight residual 200.00 46.79 153.21 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' C B 35 " pdb=" C1' C B 35 " pdb=" N1 C B 35 " pdb=" C2 C B 35 " ideal model delta sinusoidal sigma weight residual 200.00 50.92 149.08 1 1.50e+01 4.44e-03 7.93e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1307 0.065 - 0.129: 166 0.129 - 0.193: 26 0.193 - 0.258: 3 0.258 - 0.322: 4 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CG LEU A 305 " pdb=" CB LEU A 305 " pdb=" CD1 LEU A 305 " pdb=" CD2 LEU A 305 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB THR A 802 " pdb=" CA THR A 802 " pdb=" OG1 THR A 802 " pdb=" CG2 THR A 802 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1' G B 21 " pdb=" O4' G B 21 " pdb=" C2' G B 21 " pdb=" N9 G B 21 " both_signs ideal model delta sigma weight residual False 2.46 2.17 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1503 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 877 " -0.059 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO A 878 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 878 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 878 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 46 " 0.037 2.00e-02 2.50e+03 1.72e-02 8.13e+00 pdb=" N9 A B 46 " -0.039 2.00e-02 2.50e+03 pdb=" C8 A B 46 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 46 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B 46 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 46 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A B 46 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A B 46 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A B 46 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A B 46 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A B 46 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 843 " 0.013 2.00e-02 2.50e+03 1.66e-02 5.49e+00 pdb=" CG TYR A 843 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 843 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 843 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 843 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 843 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 843 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 843 " -0.004 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1249 2.75 - 3.29: 8803 3.29 - 3.83: 16158 3.83 - 4.36: 18502 4.36 - 4.90: 31292 Nonbonded interactions: 76004 Sorted by model distance: nonbonded pdb=" O2' G B 41 " pdb=" O2 U B 42 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR A 986 " pdb=" O LYS A1196 " model vdw 2.250 2.440 nonbonded pdb=" OG SER A 913 " pdb=" N ASP A 914 " model vdw 2.279 2.520 nonbonded pdb=" O SER A1019 " pdb=" OG SER A1019 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR A 910 " pdb=" O LEU A1018 " model vdw 2.316 2.440 ... (remaining 75999 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.240 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.004 0.053 9910 Z= 0.270 Angle : 0.810 11.377 13592 Z= 0.434 Chirality : 0.048 0.322 1506 Planarity : 0.006 0.090 1548 Dihedral : 22.251 178.449 4202 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 1.43 % Allowed : 29.09 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1007 helix: 0.52 (0.19), residues: 654 sheet: -1.03 (0.99), residues: 30 loop : -2.91 (0.29), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1125 HIS 0.007 0.001 HIS A 958 PHE 0.020 0.002 PHE A 909 TYR 0.041 0.002 TYR A 843 ARG 0.018 0.001 ARG A 949 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8650 (m-30) cc_final: 0.8329 (m-30) outliers start: 13 outliers final: 2 residues processed: 93 average time/residue: 1.2501 time to fit residues: 125.1664 Evaluate side-chains 74 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 919 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 366 GLN A 838 GLN A1168 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9910 Z= 0.211 Angle : 0.582 6.422 13592 Z= 0.306 Chirality : 0.040 0.246 1506 Planarity : 0.004 0.074 1548 Dihedral : 20.435 177.258 2007 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.40 % Allowed : 27.88 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1007 helix: 1.65 (0.20), residues: 664 sheet: -1.58 (1.09), residues: 20 loop : -2.53 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 887 HIS 0.005 0.001 HIS A 958 PHE 0.017 0.001 PHE A 909 TYR 0.014 0.001 TYR A 344 ARG 0.007 0.000 ARG A 949 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 1.018 Fit side-chains REVERT: A 732 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7777 (ttmt) REVERT: A 733 GLN cc_start: 0.7870 (mt0) cc_final: 0.7597 (mt0) REVERT: A 830 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: A 977 CYS cc_start: 0.6731 (m) cc_final: 0.6485 (m) outliers start: 31 outliers final: 5 residues processed: 105 average time/residue: 1.3536 time to fit residues: 151.8243 Evaluate side-chains 80 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 HIS A 503 ASN A 838 GLN A1194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9910 Z= 0.276 Angle : 0.612 7.108 13592 Z= 0.319 Chirality : 0.042 0.288 1506 Planarity : 0.004 0.065 1548 Dihedral : 20.537 176.114 2003 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.29 % Allowed : 29.09 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.75 (0.27), residues: 1007 helix: 1.89 (0.20), residues: 668 sheet: -1.31 (0.91), residues: 30 loop : -2.59 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 PHE 0.019 0.001 PHE A 909 TYR 0.017 0.002 TYR A 344 ARG 0.007 0.000 ARG A 949 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 0.986 Fit side-chains REVERT: A 275 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7782 (ptm160) REVERT: A 732 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7888 (ttpt) REVERT: A 830 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6364 (pm20) REVERT: A 977 CYS cc_start: 0.6895 (m) cc_final: 0.6675 (m) outliers start: 30 outliers final: 9 residues processed: 100 average time/residue: 1.3749 time to fit residues: 146.9539 Evaluate side-chains 81 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9910 Z= 0.176 Angle : 0.548 7.191 13592 Z= 0.287 Chirality : 0.039 0.225 1506 Planarity : 0.004 0.055 1548 Dihedral : 20.320 176.860 2003 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.40 % Allowed : 29.31 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1007 helix: 2.26 (0.20), residues: 665 sheet: -1.38 (0.89), residues: 30 loop : -2.58 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 887 HIS 0.003 0.001 HIS A 958 PHE 0.013 0.001 PHE A 909 TYR 0.011 0.001 TYR A 671 ARG 0.007 0.000 ARG A 949 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 78 time to evaluate : 1.129 Fit side-chains REVERT: A 732 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7845 (ttpt) REVERT: A 746 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7433 (ttt-90) REVERT: A 830 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6226 (pm20) REVERT: A 977 CYS cc_start: 0.6822 (m) cc_final: 0.6598 (m) outliers start: 31 outliers final: 12 residues processed: 105 average time/residue: 1.3470 time to fit residues: 151.2708 Evaluate side-chains 84 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 1068 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.0020 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9910 Z= 0.126 Angle : 0.517 7.367 13592 Z= 0.270 Chirality : 0.037 0.205 1506 Planarity : 0.003 0.047 1548 Dihedral : 20.120 178.780 2003 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.96 % Allowed : 30.30 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.28), residues: 1007 helix: 2.60 (0.20), residues: 659 sheet: -1.32 (0.92), residues: 30 loop : -2.46 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 887 HIS 0.002 0.000 HIS A 958 PHE 0.008 0.001 PHE A 909 TYR 0.009 0.001 TYR A 671 ARG 0.007 0.000 ARG A 949 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 1.141 Fit side-chains REVERT: A 751 GLU cc_start: 0.7648 (tp30) cc_final: 0.7047 (mm-30) REVERT: A 830 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6154 (pm20) REVERT: A 900 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: A 977 CYS cc_start: 0.6856 (m) cc_final: 0.6628 (m) outliers start: 27 outliers final: 9 residues processed: 101 average time/residue: 1.2896 time to fit residues: 140.2546 Evaluate side-chains 87 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9910 Z= 0.365 Angle : 0.651 7.556 13592 Z= 0.340 Chirality : 0.044 0.320 1506 Planarity : 0.004 0.045 1548 Dihedral : 20.454 177.945 2003 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 3.95 % Allowed : 30.19 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.01 (0.27), residues: 1007 helix: 2.17 (0.20), residues: 663 sheet: -1.44 (0.90), residues: 30 loop : -2.60 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 887 HIS 0.004 0.001 HIS A 673 PHE 0.020 0.002 PHE A 909 TYR 0.020 0.002 TYR A 344 ARG 0.007 0.000 ARG A 949 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 75 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5490 (OUTLIER) cc_final: 0.5057 (pmm150) REVERT: A 746 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7525 (ttt-90) REVERT: A 830 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: A 900 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: A 977 CYS cc_start: 0.6929 (m) cc_final: 0.6706 (m) outliers start: 36 outliers final: 15 residues processed: 104 average time/residue: 1.4436 time to fit residues: 160.4002 Evaluate side-chains 89 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8275 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9910 Z= 0.154 Angle : 0.546 8.276 13592 Z= 0.284 Chirality : 0.038 0.194 1506 Planarity : 0.003 0.046 1548 Dihedral : 20.226 176.862 2003 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.74 % Allowed : 30.85 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.27), residues: 1007 helix: 2.50 (0.20), residues: 659 sheet: -1.35 (0.91), residues: 30 loop : -2.55 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 887 HIS 0.003 0.001 HIS A 500 PHE 0.009 0.001 PHE A1099 TYR 0.011 0.001 TYR A 671 ARG 0.009 0.000 ARG A 949 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 1.275 Fit side-chains REVERT: A 175 ARG cc_start: 0.5502 (OUTLIER) cc_final: 0.5162 (pmm150) REVERT: A 587 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: A 751 GLU cc_start: 0.7726 (tp30) cc_final: 0.7135 (mm-30) REVERT: A 830 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6236 (pm20) REVERT: A 900 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: A 977 CYS cc_start: 0.6957 (m) cc_final: 0.6739 (m) outliers start: 25 outliers final: 11 residues processed: 99 average time/residue: 1.3687 time to fit residues: 145.2424 Evaluate side-chains 90 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9910 Z= 0.147 Angle : 0.533 8.341 13592 Z= 0.278 Chirality : 0.038 0.183 1506 Planarity : 0.003 0.041 1548 Dihedral : 20.212 178.085 2003 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.31 % Allowed : 30.74 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1007 helix: 2.64 (0.20), residues: 659 sheet: -1.24 (0.93), residues: 30 loop : -2.44 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 887 HIS 0.002 0.000 HIS A1194 PHE 0.009 0.001 PHE A 909 TYR 0.010 0.001 TYR A 671 ARG 0.010 0.000 ARG A 949 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.094 Fit side-chains REVERT: A 175 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.5124 (pmm150) REVERT: A 751 GLU cc_start: 0.7696 (tp30) cc_final: 0.7067 (mm-30) REVERT: A 830 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6173 (pm20) REVERT: A 977 CYS cc_start: 0.6832 (m) cc_final: 0.6586 (m) outliers start: 21 outliers final: 11 residues processed: 99 average time/residue: 1.2377 time to fit residues: 131.9854 Evaluate side-chains 87 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 503 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9910 Z= 0.217 Angle : 0.582 8.498 13592 Z= 0.302 Chirality : 0.040 0.250 1506 Planarity : 0.003 0.041 1548 Dihedral : 20.230 176.598 2003 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.52 % Allowed : 30.52 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 1007 helix: 2.54 (0.20), residues: 660 sheet: -1.32 (0.92), residues: 30 loop : -2.52 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 887 HIS 0.002 0.001 HIS A 673 PHE 0.013 0.001 PHE A 909 TYR 0.013 0.001 TYR A 344 ARG 0.011 0.000 ARG A 949 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 1.121 Fit side-chains REVERT: A 175 ARG cc_start: 0.5494 (OUTLIER) cc_final: 0.5104 (pmm150) REVERT: A 751 GLU cc_start: 0.7686 (tp30) cc_final: 0.7124 (mm-30) REVERT: A 830 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6188 (pm20) REVERT: A 900 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: A 977 CYS cc_start: 0.6850 (m) cc_final: 0.6622 (m) outliers start: 23 outliers final: 13 residues processed: 93 average time/residue: 1.3260 time to fit residues: 132.2242 Evaluate side-chains 86 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9910 Z= 0.148 Angle : 0.566 9.765 13592 Z= 0.294 Chirality : 0.038 0.188 1506 Planarity : 0.003 0.046 1548 Dihedral : 20.175 177.752 2003 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.87 % Allowed : 31.06 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1007 helix: 2.64 (0.20), residues: 660 sheet: -1.22 (0.93), residues: 30 loop : -2.40 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 887 HIS 0.002 0.000 HIS A1194 PHE 0.008 0.001 PHE A 771 TYR 0.011 0.001 TYR A 671 ARG 0.011 0.000 ARG A 949 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.5134 (pmm150) REVERT: A 751 GLU cc_start: 0.7673 (tp30) cc_final: 0.7102 (mm-30) REVERT: A 830 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6145 (pm20) REVERT: A 900 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: A 977 CYS cc_start: 0.6886 (m) cc_final: 0.6658 (m) outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 1.3662 time to fit residues: 137.7701 Evaluate side-chains 87 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.156823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.116342 restraints weight = 12663.021| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.31 r_work: 0.3235 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9910 Z= 0.243 Angle : 0.625 9.104 13592 Z= 0.320 Chirality : 0.041 0.260 1506 Planarity : 0.004 0.060 1548 Dihedral : 20.243 176.275 2003 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 1.87 % Allowed : 31.72 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1007 helix: 2.48 (0.20), residues: 660 sheet: -1.27 (0.92), residues: 30 loop : -2.53 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 887 HIS 0.003 0.001 HIS A 673 PHE 0.012 0.001 PHE A 909 TYR 0.019 0.002 TYR A 843 ARG 0.013 0.000 ARG A 992 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.96 seconds wall clock time: 54 minutes 0.79 seconds (3240.79 seconds total)