Starting phenix.real_space_refine on Sun Jul 27 21:21:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ewg_28645/07_2025/8ewg_28645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ewg_28645/07_2025/8ewg_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/cci-nas-00/data/ceres_data/8ewg_28645/07_2025/8ewg_28645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ewg_28645/07_2025/8ewg_28645.map" model { file = "/net/cci-nas-00/data/ceres_data/8ewg_28645/07_2025/8ewg_28645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ewg_28645/07_2025/8ewg_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. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.19, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 995.0 milliseconds 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: 3.05 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: 3.58 Time building geometry restraints manager: 2.88 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: 0.00 - 2.28: 13273 2.28 - 4.55: 259 4.55 - 6.83: 45 6.83 - 9.10: 11 9.10 - 11.38: 4 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 3.040 nonbonded pdb=" OH TYR A 986 " pdb=" O LYS A1196 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 913 " pdb=" N ASP A 914 " model vdw 2.279 3.120 nonbonded pdb=" O SER A1019 " pdb=" OG SER A1019 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 910 " pdb=" O LEU A1018 " model vdw 2.316 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.620 Find NCS groups from input model: 0.100 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.750 ------------------------------------------------------------------------------- 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= 0.207 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 Details of bonding type rmsd hydrogen bonds : bond 0.15338 ( 497) hydrogen bonds : angle 4.98969 ( 1433) covalent geometry : bond 0.00425 ( 9910) covalent geometry : angle 0.81046 (13592) *********************** 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 to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.934 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: 1.2809 time to fit residues: 127.8640 Evaluate side-chains 74 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 3.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 838 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.161295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121145 restraints weight = 12647.818| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.35 r_work: 0.3309 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9910 Z= 0.122 Angle : 0.562 6.221 13592 Z= 0.296 Chirality : 0.039 0.206 1506 Planarity : 0.004 0.073 1548 Dihedral : 20.311 178.639 2007 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.29 % Allowed : 27.22 % 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: 0.56 (0.27), residues: 1007 helix: 1.71 (0.20), residues: 664 sheet: -1.49 (1.11), residues: 20 loop : -2.49 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 PHE 0.014 0.001 PHE A 909 TYR 0.010 0.001 TYR A 344 ARG 0.008 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.06196 ( 497) hydrogen bonds : angle 3.44885 ( 1433) covalent geometry : bond 0.00248 ( 9910) covalent geometry : angle 0.56168 (13592) *********************** 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 115 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 1.052 Fit side-chains REVERT: A 445 LYS cc_start: 0.8490 (tmtm) cc_final: 0.8289 (tmmm) REVERT: A 732 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7485 (ttpt) REVERT: A 733 GLN cc_start: 0.8056 (mt0) cc_final: 0.7810 (mt0) REVERT: A 830 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6242 (pm20) REVERT: A 977 CYS cc_start: 0.7135 (m) cc_final: 0.6875 (m) outliers start: 30 outliers final: 6 residues processed: 106 average time/residue: 1.3353 time to fit residues: 151.4575 Evaluate side-chains 82 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 LEU 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 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 1154 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 A1058 GLN A1168 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114431 restraints weight = 12849.772| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.36 r_work: 0.3214 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9910 Z= 0.205 Angle : 0.634 9.127 13592 Z= 0.330 Chirality : 0.043 0.312 1506 Planarity : 0.004 0.065 1548 Dihedral : 20.397 176.252 2003 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.24 % Favored : 91.66 % Rotamer: Outliers : 2.85 % Allowed : 28.87 % Favored : 68.28 % 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: 0.73 (0.27), residues: 1007 helix: 1.85 (0.20), residues: 668 sheet: -1.20 (0.94), residues: 30 loop : -2.55 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 PHE 0.020 0.002 PHE A 909 TYR 0.017 0.002 TYR A 344 ARG 0.008 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.06860 ( 497) hydrogen bonds : angle 3.49224 ( 1433) covalent geometry : bond 0.00474 ( 9910) covalent geometry : angle 0.63421 (13592) *********************** 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 to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 732 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7682 (ttpt) REVERT: A 733 GLN cc_start: 0.8150 (mt0) cc_final: 0.7936 (mt0) REVERT: A 830 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6477 (pm20) REVERT: A 977 CYS cc_start: 0.7216 (m) cc_final: 0.6962 (m) outliers start: 26 outliers final: 7 residues processed: 101 average time/residue: 1.3677 time to fit residues: 147.4522 Evaluate side-chains 75 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 469 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN A 622 GLN A 838 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.158155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117819 restraints weight = 12759.791| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.32 r_work: 0.3269 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1686 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= 0.127 Angle : 0.560 7.665 13592 Z= 0.292 Chirality : 0.039 0.222 1506 Planarity : 0.003 0.055 1548 Dihedral : 20.185 177.176 2003 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.52 % Allowed : 29.42 % Favored : 68.06 % 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: 1.17 (0.27), residues: 1007 helix: 2.26 (0.20), residues: 664 sheet: -1.23 (0.94), residues: 30 loop : -2.50 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 PHE 0.013 0.001 PHE A 909 TYR 0.012 0.001 TYR A 910 ARG 0.007 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.05781 ( 497) hydrogen bonds : angle 3.26329 ( 1433) covalent geometry : bond 0.00270 ( 9910) covalent geometry : angle 0.56021 (13592) *********************** 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 103 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8433 (tmtm) cc_final: 0.8207 (tmmm) REVERT: A 556 ASP cc_start: 0.7803 (p0) cc_final: 0.7557 (p0) REVERT: A 718 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: A 732 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7572 (ttpt) REVERT: A 830 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6347 (pm20) REVERT: A 977 CYS cc_start: 0.7226 (m) cc_final: 0.6978 (m) REVERT: A 1106 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7877 (tppt) REVERT: A 1200 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6873 (mp) REVERT: A 1214 ASP cc_start: 0.8122 (m-30) cc_final: 0.7869 (m-30) outliers start: 23 outliers final: 6 residues processed: 98 average time/residue: 1.3288 time to fit residues: 139.1643 Evaluate side-chains 85 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 0.0370 chunk 27 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 0.5870 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.161719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122333 restraints weight = 12653.922| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.29 r_work: 0.3321 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9910 Z= 0.104 Angle : 0.529 8.367 13592 Z= 0.276 Chirality : 0.037 0.208 1506 Planarity : 0.003 0.045 1548 Dihedral : 19.992 179.240 2003 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.31 % Allowed : 29.31 % Favored : 68.39 % 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: 1.50 (0.28), residues: 1007 helix: 2.57 (0.20), residues: 658 sheet: -1.24 (0.95), residues: 30 loop : -2.38 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 887 HIS 0.003 0.000 HIS A1194 PHE 0.010 0.001 PHE A 909 TYR 0.011 0.001 TYR A 843 ARG 0.008 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.05041 ( 497) hydrogen bonds : angle 3.10165 ( 1433) covalent geometry : bond 0.00209 ( 9910) covalent geometry : angle 0.52882 (13592) *********************** 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 106 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5276 (OUTLIER) cc_final: 0.4926 (pmm150) REVERT: A 445 LYS cc_start: 0.8447 (tmtm) cc_final: 0.8229 (tmmm) REVERT: A 732 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7615 (ttpt) REVERT: A 830 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6255 (pm20) REVERT: A 900 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: A 977 CYS cc_start: 0.7278 (m) cc_final: 0.7023 (m) REVERT: A 1106 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7781 (tppt) REVERT: A 1200 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6824 (mp) REVERT: A 1214 ASP cc_start: 0.8144 (m-30) cc_final: 0.7906 (m-30) outliers start: 21 outliers final: 5 residues processed: 97 average time/residue: 1.3777 time to fit residues: 143.0267 Evaluate side-chains 88 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG 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 551 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 900 GLU 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 79 optimal weight: 2.9990 chunk 1 optimal weight: 0.0270 chunk 70 optimal weight: 0.3980 chunk 6 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 overall best weight: 2.6844 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.155130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114099 restraints weight = 12790.677| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.37 r_work: 0.3206 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9910 Z= 0.196 Angle : 0.614 8.373 13592 Z= 0.320 Chirality : 0.042 0.300 1506 Planarity : 0.004 0.042 1548 Dihedral : 20.163 176.603 2003 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.07 % Allowed : 28.98 % Favored : 67.95 % 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: 1.24 (0.27), residues: 1007 helix: 2.32 (0.20), residues: 663 sheet: -1.35 (0.93), residues: 30 loop : -2.43 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 PHE 0.015 0.002 PHE A 909 TYR 0.018 0.002 TYR A 344 ARG 0.009 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.06513 ( 497) hydrogen bonds : angle 3.31250 ( 1433) covalent geometry : bond 0.00450 ( 9910) covalent geometry : angle 0.61403 (13592) *********************** 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 106 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5338 (OUTLIER) cc_final: 0.4987 (pmm150) REVERT: A 556 ASP cc_start: 0.7947 (p0) cc_final: 0.7730 (p0) REVERT: A 732 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7691 (ttpt) REVERT: A 746 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7409 (ttt-90) REVERT: A 830 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6422 (pm20) REVERT: A 900 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: A 977 CYS cc_start: 0.7298 (m) cc_final: 0.7053 (m) REVERT: A 1106 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7956 (tppt) REVERT: A 1200 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6848 (mp) REVERT: A 1214 ASP cc_start: 0.8168 (m-30) cc_final: 0.7916 (m-30) outliers start: 28 outliers final: 6 residues processed: 98 average time/residue: 1.3673 time to fit residues: 143.5894 Evaluate side-chains 85 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG 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 551 LEU 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 884 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 900 GLU 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 36 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.159711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119950 restraints weight = 12784.601| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.33 r_work: 0.3297 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9910 Z= 0.113 Angle : 0.552 8.613 13592 Z= 0.287 Chirality : 0.038 0.190 1506 Planarity : 0.003 0.038 1548 Dihedral : 20.037 177.943 2003 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.41 % Allowed : 29.97 % Favored : 67.62 % 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: 1.50 (0.27), residues: 1007 helix: 2.57 (0.20), residues: 658 sheet: -1.37 (0.93), residues: 30 loop : -2.39 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 PHE 0.008 0.001 PHE A 909 TYR 0.017 0.001 TYR A 843 ARG 0.008 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 497) hydrogen bonds : angle 3.14905 ( 1433) covalent geometry : bond 0.00236 ( 9910) covalent geometry : angle 0.55219 (13592) *********************** 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 102 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5430 (OUTLIER) cc_final: 0.5063 (pmm150) REVERT: A 445 LYS cc_start: 0.8505 (tmtm) cc_final: 0.8276 (tmmm) REVERT: A 587 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: A 732 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7473 (ttmt) REVERT: A 830 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: A 900 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: A 977 CYS cc_start: 0.7291 (m) cc_final: 0.7051 (m) REVERT: A 1106 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7820 (tppt) REVERT: A 1200 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6859 (mp) REVERT: A 1214 ASP cc_start: 0.8158 (m-30) cc_final: 0.7879 (m-30) REVERT: A 1220 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8485 (mmp) outliers start: 22 outliers final: 8 residues processed: 94 average time/residue: 1.4535 time to fit residues: 146.0354 Evaluate side-chains 89 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 587 GLU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 1154 MET Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1220 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.156838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115757 restraints weight = 12884.893| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.40 r_work: 0.3236 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9910 Z= 0.152 Angle : 0.587 8.829 13592 Z= 0.305 Chirality : 0.040 0.256 1506 Planarity : 0.003 0.038 1548 Dihedral : 20.084 176.990 2003 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.20 % Allowed : 30.08 % Favored : 67.73 % 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: 1.42 (0.27), residues: 1007 helix: 2.49 (0.20), residues: 663 sheet: -1.43 (0.92), residues: 30 loop : -2.46 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 PHE 0.012 0.001 PHE A 909 TYR 0.020 0.002 TYR A 843 ARG 0.010 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.06042 ( 497) hydrogen bonds : angle 3.21713 ( 1433) covalent geometry : bond 0.00342 ( 9910) covalent geometry : angle 0.58702 (13592) *********************** 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 95 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.5029 (pmm150) REVERT: A 556 ASP cc_start: 0.7846 (p0) cc_final: 0.7580 (p0) REVERT: A 718 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: A 732 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7611 (ttmt) REVERT: A 830 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6378 (pm20) REVERT: A 900 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: A 977 CYS cc_start: 0.7260 (m) cc_final: 0.7017 (m) REVERT: A 1106 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7893 (tppt) REVERT: A 1200 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6777 (mp) REVERT: A 1214 ASP cc_start: 0.8156 (m-30) cc_final: 0.7915 (m-30) outliers start: 20 outliers final: 8 residues processed: 91 average time/residue: 1.3269 time to fit residues: 129.7794 Evaluate side-chains 84 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 309 LEU 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 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 900 GLU 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 72 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.154146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112851 restraints weight = 12727.473| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.39 r_work: 0.3188 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9910 Z= 0.211 Angle : 0.651 8.992 13592 Z= 0.338 Chirality : 0.043 0.301 1506 Planarity : 0.004 0.043 1548 Dihedral : 20.208 176.961 2003 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.94 % Favored : 90.96 % Rotamer: Outliers : 2.41 % Allowed : 29.86 % Favored : 67.73 % 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: 1.10 (0.27), residues: 1007 helix: 2.23 (0.20), residues: 664 sheet: -1.40 (0.92), residues: 30 loop : -2.57 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 887 HIS 0.005 0.001 HIS A1194 PHE 0.018 0.002 PHE A 909 TYR 0.026 0.002 TYR A 843 ARG 0.010 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.06721 ( 497) hydrogen bonds : angle 3.38892 ( 1433) covalent geometry : bond 0.00491 ( 9910) covalent geometry : angle 0.65118 (13592) *********************** 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 101 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5416 (OUTLIER) cc_final: 0.5049 (pmm150) REVERT: A 405 ASN cc_start: 0.7961 (t0) cc_final: 0.7735 (t0) REVERT: A 556 ASP cc_start: 0.7952 (p0) cc_final: 0.7748 (p0) REVERT: A 718 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 732 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7661 (ttmt) REVERT: A 746 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7459 (ttt-90) REVERT: A 830 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: A 900 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: A 949 ARG cc_start: 0.6974 (mtm110) cc_final: 0.6736 (mtm180) REVERT: A 977 CYS cc_start: 0.7313 (m) cc_final: 0.7072 (m) REVERT: A 1106 LYS cc_start: 0.8258 (ttmm) cc_final: 0.8000 (tppt) REVERT: A 1200 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6774 (mp) outliers start: 22 outliers final: 8 residues processed: 96 average time/residue: 1.7434 time to fit residues: 178.8321 Evaluate side-chains 86 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 309 LEU 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 718 GLU 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 884 GLU Chi-restraints excluded: chain A residue 900 GLU 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 63 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 92 optimal weight: 0.0970 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.159416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119157 restraints weight = 12804.624| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.36 r_work: 0.3287 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9910 Z= 0.115 Angle : 0.568 9.089 13592 Z= 0.296 Chirality : 0.038 0.192 1506 Planarity : 0.003 0.040 1548 Dihedral : 20.070 177.401 2003 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.87 % Allowed : 30.52 % Favored : 67.62 % 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: 1.46 (0.27), residues: 1007 helix: 2.55 (0.20), residues: 659 sheet: -1.35 (0.94), residues: 30 loop : -2.44 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 PHE 0.008 0.001 PHE A 909 TYR 0.025 0.001 TYR A 843 ARG 0.010 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 497) hydrogen bonds : angle 3.18153 ( 1433) covalent geometry : bond 0.00245 ( 9910) covalent geometry : angle 0.56783 (13592) ********************** 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 97 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.5047 (pmm150) REVERT: A 405 ASN cc_start: 0.7930 (t0) cc_final: 0.7713 (t0) REVERT: A 445 LYS cc_start: 0.8456 (tmtm) cc_final: 0.8233 (tmmm) REVERT: A 556 ASP cc_start: 0.7810 (p0) cc_final: 0.7538 (p0) REVERT: A 587 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: A 718 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: A 732 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7460 (ttmt) REVERT: A 751 GLU cc_start: 0.7970 (tp30) cc_final: 0.7256 (pm20) REVERT: A 830 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6335 (pm20) REVERT: A 900 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: A 977 CYS cc_start: 0.7319 (m) cc_final: 0.7085 (m) REVERT: A 1106 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7822 (tppt) REVERT: A 1200 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6832 (mp) REVERT: A 1214 ASP cc_start: 0.8116 (m-30) cc_final: 0.7914 (m-30) outliers start: 17 outliers final: 7 residues processed: 93 average time/residue: 1.3452 time to fit residues: 134.2013 Evaluate side-chains 89 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 587 GLU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 900 GLU 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 92 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.155552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115089 restraints weight = 12782.858| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.32 r_work: 0.3225 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2285 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= 0.171 Angle : 0.613 9.088 13592 Z= 0.319 Chirality : 0.041 0.271 1506 Planarity : 0.004 0.043 1548 Dihedral : 20.125 176.208 2003 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 1.87 % Allowed : 30.19 % Favored : 67.95 % 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: 1.32 (0.27), residues: 1007 helix: 2.41 (0.20), residues: 664 sheet: -1.51 (0.93), residues: 30 loop : -2.48 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 887 HIS 0.005 0.001 HIS A1194 PHE 0.014 0.001 PHE A 909 TYR 0.032 0.002 TYR A 843 ARG 0.011 0.000 ARG A 949 Details of bonding type rmsd hydrogen bonds : bond 0.06025 ( 497) hydrogen bonds : angle 3.27889 ( 1433) covalent geometry : bond 0.00396 ( 9910) covalent geometry : angle 0.61328 (13592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5751.88 seconds wall clock time: 100 minutes 3.34 seconds (6003.34 seconds total)