Starting phenix.real_space_refine on Tue Mar 3 23:54:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whn_32505/03_2026/7whn_32505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whn_32505/03_2026/7whn_32505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7whn_32505/03_2026/7whn_32505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whn_32505/03_2026/7whn_32505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7whn_32505/03_2026/7whn_32505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whn_32505/03_2026/7whn_32505.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5816 2.51 5 N 1629 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9284 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9284 Classifications: {'peptide': 1170} Link IDs: {'PCIS': 4, 'PTRANS': 38, 'TRANS': 1127} Time building chain proxies: 2.01, per 1000 atoms: 0.22 Number of scatterers: 9284 At special positions: 0 Unit cell: (92.394, 98.766, 210.276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1800 8.00 N 1629 7.00 C 5816 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: 0.69 Conformation dependent library (CDL) restraints added in 384.9 milliseconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 9 sheets defined 35.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 28 through 53 Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 306 through 338 removed outlier: 3.910A pdb=" N HIS A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 372 removed outlier: 3.806A pdb=" N ARG A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 652 through 658 Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.688A pdb=" N ASN A 688 " --> pdb=" O TYR A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 754 Processing helix chain 'A' and resid 756 through 772 removed outlier: 4.306A pdb=" N GLY A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 771 " --> pdb=" O GLN A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 777 removed outlier: 3.627A pdb=" N LEU A 777 " --> pdb=" O ASP A 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 774 through 777' Processing helix chain 'A' and resid 778 through 796 removed outlier: 3.611A pdb=" N SER A 796 " --> pdb=" O MET A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 815 removed outlier: 3.690A pdb=" N ILE A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 835 Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.578A pdb=" N THR A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 861 removed outlier: 4.090A pdb=" N GLY A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 885 Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 897 through 901 Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 909 through 923 removed outlier: 3.606A pdb=" N PHE A 922 " --> pdb=" O MET A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 938 removed outlier: 3.873A pdb=" N ARG A 938 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 994 Processing helix chain 'A' and resid 1036 through 1040 Processing helix chain 'A' and resid 1074 through 1087 Processing helix chain 'A' and resid 1094 through 1107 removed outlier: 3.528A pdb=" N VAL A1106 " --> pdb=" O ILE A1102 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A1107 " --> pdb=" O SER A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1136 removed outlier: 3.593A pdb=" N LEU A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1148 through 1161 removed outlier: 4.119A pdb=" N PHE A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A1153 " --> pdb=" O CYS A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1194 removed outlier: 4.322A pdb=" N ALA A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.949A pdb=" N ASN A 105 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 106 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU A 231 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 263 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 233 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 181 removed outlier: 6.455A pdb=" N ASP A 155 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 149 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU A 157 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN A 124 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 125 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 284 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE A 127 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 214 removed outlier: 4.133A pdb=" N ASN A1053 " --> pdb=" O ILE A1062 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A1062 " --> pdb=" O ASN A1053 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 300 " --> pdb=" O ILE A1063 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ARG A1065 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 214 removed outlier: 6.731A pdb=" N SER A1016 " --> pdb=" O GLU A1012 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 384 removed outlier: 4.160A pdb=" N LEU A 379 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 736 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 394 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 728 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY A 392 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 730 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLY A 732 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP A 388 " --> pdb=" O GLY A 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 379 through 384 removed outlier: 4.160A pdb=" N LEU A 379 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 736 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 729 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU A 567 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS A 731 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER A 565 " --> pdb=" O HIS A 731 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 733 " --> pdb=" O ARG A 563 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A 737 " --> pdb=" O ASP A 559 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ASP A 559 " --> pdb=" O ARG A 737 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 408 removed outlier: 3.613A pdb=" N TYR A 407 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 439 " --> pdb=" O PHE A 676 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 441 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.819A pdb=" N PHE A 468 " --> pdb=" O HIS A 452 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 467 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU A 545 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER A 469 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL A 543 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 545 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 602 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 547 " --> pdb=" O CYS A 600 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N CYS A 600 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLY A 549 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU A 598 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 864 through 865 removed outlier: 6.633A pdb=" N ASN A 864 " --> pdb=" O GLU A1119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 404 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 0.92 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: 2732 1.33 - 1.45: 1440 1.45 - 1.57: 5209 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9455 Sorted by residual: bond pdb=" CB ASN A1030 " pdb=" CG ASN A1030 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.11e+00 bond pdb=" C GLU A 679 " pdb=" N LEU A 680 " ideal model delta sigma weight residual 1.325 1.345 -0.020 1.25e-02 6.40e+03 2.67e+00 bond pdb=" CG GLN A1179 " pdb=" CD GLN A1179 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.42e+00 bond pdb=" CB ASP A 182 " pdb=" CG ASP A 182 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.38e+00 bond pdb=" CB ASP A 756 " pdb=" CG ASP A 756 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.34e+00 ... (remaining 9450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 12083 1.59 - 3.17: 656 3.17 - 4.76: 75 4.76 - 6.34: 12 6.34 - 7.93: 2 Bond angle restraints: 12828 Sorted by residual: angle pdb=" N GLY A 815 " pdb=" CA GLY A 815 " pdb=" C GLY A 815 " ideal model delta sigma weight residual 114.92 120.28 -5.36 1.30e+00 5.92e-01 1.70e+01 angle pdb=" CA LEU A 777 " pdb=" C LEU A 777 " pdb=" N ASN A 778 " ideal model delta sigma weight residual 118.27 112.71 5.56 1.59e+00 3.96e-01 1.22e+01 angle pdb=" C LEU A 240 " pdb=" N HIS A 241 " pdb=" CA HIS A 241 " ideal model delta sigma weight residual 122.21 117.99 4.22 1.48e+00 4.57e-01 8.11e+00 angle pdb=" N VAL A 532 " pdb=" CA VAL A 532 " pdb=" C VAL A 532 " ideal model delta sigma weight residual 107.71 111.90 -4.19 1.58e+00 4.01e-01 7.02e+00 angle pdb=" N ASP A 629 " pdb=" CA ASP A 629 " pdb=" C ASP A 629 " ideal model delta sigma weight residual 111.36 114.08 -2.72 1.09e+00 8.42e-01 6.24e+00 ... (remaining 12823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5139 16.96 - 33.91: 489 33.91 - 50.86: 77 50.86 - 67.82: 18 67.82 - 84.77: 7 Dihedral angle restraints: 5730 sinusoidal: 2307 harmonic: 3423 Sorted by residual: dihedral pdb=" CA ILE A 730 " pdb=" C ILE A 730 " pdb=" N HIS A 731 " pdb=" CA HIS A 731 " ideal model delta harmonic sigma weight residual 180.00 156.63 23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLN A 755 " pdb=" C GLN A 755 " pdb=" N ASP A 756 " pdb=" CA ASP A 756 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA HIS A 136 " pdb=" C HIS A 136 " pdb=" N PHE A 137 " pdb=" CA PHE A 137 " ideal model delta harmonic sigma weight residual -180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 831 0.040 - 0.081: 448 0.081 - 0.121: 151 0.121 - 0.162: 32 0.162 - 0.202: 2 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CB THR A1007 " pdb=" CA THR A1007 " pdb=" OG1 THR A1007 " pdb=" CG2 THR A1007 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU A 240 " pdb=" CB LEU A 240 " pdb=" CD1 LEU A 240 " pdb=" CD2 LEU A 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CB ILE A1063 " pdb=" CA ILE A1063 " pdb=" CG1 ILE A1063 " pdb=" CG2 ILE A1063 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1461 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 952 " -0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO A 953 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 953 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 953 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 234 " -0.011 2.00e-02 2.50e+03 1.26e-02 3.19e+00 pdb=" CG TYR A 234 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 234 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 234 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 234 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 234 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 234 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 234 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 600 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 601 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 601 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 601 " 0.025 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 280 2.70 - 3.25: 8660 3.25 - 3.80: 13899 3.80 - 4.35: 17952 4.35 - 4.90: 30950 Nonbonded interactions: 71741 Sorted by model distance: nonbonded pdb=" OH TYR A 176 " pdb=" OG SER A 237 " model vdw 2.147 3.040 nonbonded pdb=" O SER A 614 " pdb=" NH2 ARG A 698 " model vdw 2.207 3.120 nonbonded pdb=" O ILE A 546 " pdb=" OG1 THR A 599 " model vdw 2.247 3.040 nonbonded pdb=" NE2 GLN A 94 " pdb=" O LEU A 276 " model vdw 2.249 3.120 nonbonded pdb=" O ARG A 721 " pdb=" N THR A 725 " model vdw 2.270 3.120 ... (remaining 71736 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: 2.410 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.480 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.009 0.057 9455 Z= 0.368 Angle : 0.800 7.926 12828 Z= 0.470 Chirality : 0.053 0.202 1464 Planarity : 0.005 0.081 1674 Dihedral : 13.811 84.774 3522 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.22), residues: 1168 helix: 0.45 (0.26), residues: 373 sheet: -0.68 (0.32), residues: 241 loop : -1.87 (0.22), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 219 TYR 0.031 0.003 TYR A 234 PHE 0.027 0.003 PHE A1140 TRP 0.017 0.002 TRP A1099 HIS 0.007 0.002 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00877 ( 9455) covalent geometry : angle 0.80034 (12828) hydrogen bonds : bond 0.18674 ( 399) hydrogen bonds : angle 7.32140 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.341 Fit side-chains REVERT: A 182 ASP cc_start: 0.8278 (t0) cc_final: 0.7943 (t0) REVERT: A 763 ASP cc_start: 0.7674 (m-30) cc_final: 0.6880 (m-30) REVERT: A 768 GLU cc_start: 0.8162 (tp30) cc_final: 0.7191 (mt-10) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1149 time to fit residues: 15.8860 Evaluate side-chains 94 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.184105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.123309 restraints weight = 10268.089| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.86 r_work: 0.2941 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9455 Z= 0.155 Angle : 0.551 6.119 12828 Z= 0.299 Chirality : 0.045 0.150 1464 Planarity : 0.004 0.064 1674 Dihedral : 5.058 18.125 1298 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.48 % Allowed : 5.49 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.23), residues: 1168 helix: 1.20 (0.27), residues: 390 sheet: -0.42 (0.34), residues: 210 loop : -1.67 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.016 0.002 TYR A1050 PHE 0.015 0.001 PHE A 128 TRP 0.014 0.001 TRP A1099 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9455) covalent geometry : angle 0.55123 (12828) hydrogen bonds : bond 0.05296 ( 399) hydrogen bonds : angle 5.27213 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.203 Fit side-chains REVERT: A 182 ASP cc_start: 0.8264 (t0) cc_final: 0.7932 (t0) REVERT: A 763 ASP cc_start: 0.8014 (m-30) cc_final: 0.7244 (m-30) REVERT: A 872 SER cc_start: 0.9067 (t) cc_final: 0.8654 (p) outliers start: 5 outliers final: 3 residues processed: 109 average time/residue: 0.1093 time to fit residues: 15.9908 Evaluate side-chains 106 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 1117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN A 993 ASN ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.186690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.125818 restraints weight = 10248.067| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.83 r_work: 0.2978 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9455 Z= 0.109 Angle : 0.475 5.692 12828 Z= 0.256 Chirality : 0.042 0.143 1464 Planarity : 0.004 0.056 1674 Dihedral : 4.476 16.428 1298 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 7.41 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1168 helix: 1.83 (0.27), residues: 388 sheet: -0.01 (0.34), residues: 220 loop : -1.44 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.014 0.001 TYR A1050 PHE 0.014 0.001 PHE A 128 TRP 0.011 0.001 TRP A1099 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9455) covalent geometry : angle 0.47482 (12828) hydrogen bonds : bond 0.04109 ( 399) hydrogen bonds : angle 4.69335 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.329 Fit side-chains REVERT: A 182 ASP cc_start: 0.8085 (t0) cc_final: 0.7770 (t0) REVERT: A 207 ASP cc_start: 0.7778 (t0) cc_final: 0.7452 (t70) REVERT: A 283 ASP cc_start: 0.8654 (t70) cc_final: 0.8391 (t0) REVERT: A 872 SER cc_start: 0.9039 (t) cc_final: 0.8727 (p) REVERT: A 1005 THR cc_start: 0.9057 (m) cc_final: 0.8692 (p) outliers start: 7 outliers final: 4 residues processed: 111 average time/residue: 0.1113 time to fit residues: 16.8032 Evaluate side-chains 107 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS A 767 GLN A 864 ASN A1030 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.183955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.123991 restraints weight = 10367.128| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.89 r_work: 0.2943 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9455 Z= 0.164 Angle : 0.514 5.766 12828 Z= 0.275 Chirality : 0.044 0.142 1464 Planarity : 0.004 0.055 1674 Dihedral : 4.569 15.168 1298 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.25 % Allowed : 9.72 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1168 helix: 1.85 (0.27), residues: 382 sheet: -0.12 (0.32), residues: 237 loop : -1.42 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.015 0.002 TYR A1125 PHE 0.017 0.001 PHE A1003 TRP 0.013 0.001 TRP A1099 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9455) covalent geometry : angle 0.51354 (12828) hydrogen bonds : bond 0.04756 ( 399) hydrogen bonds : angle 4.65621 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.338 Fit side-chains REVERT: A 182 ASP cc_start: 0.8131 (t0) cc_final: 0.7749 (t0) REVERT: A 651 MET cc_start: 0.0619 (mpp) cc_final: -0.0247 (tpt) REVERT: A 754 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.8068 (p90) REVERT: A 763 ASP cc_start: 0.8051 (m-30) cc_final: 0.7262 (m-30) REVERT: A 866 SER cc_start: 0.8624 (t) cc_final: 0.8359 (m) REVERT: A 872 SER cc_start: 0.9103 (t) cc_final: 0.8705 (p) REVERT: A 1004 MET cc_start: 0.9040 (ttp) cc_final: 0.8818 (ttt) outliers start: 13 outliers final: 7 residues processed: 115 average time/residue: 0.1134 time to fit residues: 17.6467 Evaluate side-chains 115 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 40.0000 chunk 3 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 104 optimal weight: 0.0070 chunk 36 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.186586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.125767 restraints weight = 10290.312| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.82 r_work: 0.2981 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9455 Z= 0.097 Angle : 0.457 5.445 12828 Z= 0.245 Chirality : 0.042 0.140 1464 Planarity : 0.003 0.052 1674 Dihedral : 4.269 14.204 1298 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.96 % Allowed : 9.82 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.24), residues: 1168 helix: 2.11 (0.27), residues: 387 sheet: 0.15 (0.34), residues: 220 loop : -1.28 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.013 0.001 TYR A1050 PHE 0.014 0.001 PHE A1003 TRP 0.011 0.001 TRP A1099 HIS 0.008 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9455) covalent geometry : angle 0.45672 (12828) hydrogen bonds : bond 0.03932 ( 399) hydrogen bonds : angle 4.42001 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.338 Fit side-chains REVERT: A 182 ASP cc_start: 0.8080 (t0) cc_final: 0.7699 (t0) REVERT: A 207 ASP cc_start: 0.7812 (t0) cc_final: 0.7487 (t70) REVERT: A 283 ASP cc_start: 0.8664 (t70) cc_final: 0.8320 (t0) REVERT: A 651 MET cc_start: 0.0616 (mpp) cc_final: -0.0321 (tpt) REVERT: A 763 ASP cc_start: 0.7933 (m-30) cc_final: 0.7174 (m-30) REVERT: A 872 SER cc_start: 0.8992 (t) cc_final: 0.8675 (p) REVERT: A 1005 THR cc_start: 0.9072 (m) cc_final: 0.8710 (p) outliers start: 10 outliers final: 5 residues processed: 112 average time/residue: 0.1164 time to fit residues: 17.5394 Evaluate side-chains 113 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 51 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 43 optimal weight: 0.0070 chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS A 767 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.185875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.126166 restraints weight = 10353.801| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.83 r_work: 0.2979 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9455 Z= 0.122 Angle : 0.467 5.584 12828 Z= 0.250 Chirality : 0.042 0.138 1464 Planarity : 0.004 0.051 1674 Dihedral : 4.238 13.913 1298 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.44 % Allowed : 10.11 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1168 helix: 2.27 (0.27), residues: 380 sheet: 0.00 (0.35), residues: 219 loop : -1.10 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.014 0.001 TYR A1050 PHE 0.016 0.001 PHE A1003 TRP 0.011 0.001 TRP A1099 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9455) covalent geometry : angle 0.46713 (12828) hydrogen bonds : bond 0.04073 ( 399) hydrogen bonds : angle 4.36883 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.411 Fit side-chains REVERT: A 182 ASP cc_start: 0.8070 (t0) cc_final: 0.7684 (t0) REVERT: A 207 ASP cc_start: 0.7843 (t0) cc_final: 0.7523 (t70) REVERT: A 283 ASP cc_start: 0.8654 (t70) cc_final: 0.8359 (t0) REVERT: A 651 MET cc_start: 0.0220 (mpp) cc_final: -0.0298 (tpt) REVERT: A 754 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8193 (p90) REVERT: A 763 ASP cc_start: 0.7916 (m-30) cc_final: 0.7149 (m-30) REVERT: A 872 SER cc_start: 0.9061 (t) cc_final: 0.8737 (p) REVERT: A 1005 THR cc_start: 0.9082 (m) cc_final: 0.8717 (p) outliers start: 15 outliers final: 7 residues processed: 119 average time/residue: 0.1047 time to fit residues: 17.1094 Evaluate side-chains 116 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1058 ASP Chi-restraints excluded: chain A residue 1117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.186973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.127763 restraints weight = 10355.213| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.84 r_work: 0.2992 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9455 Z= 0.098 Angle : 0.449 5.485 12828 Z= 0.241 Chirality : 0.042 0.278 1464 Planarity : 0.003 0.050 1674 Dihedral : 4.141 13.572 1298 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.15 % Allowed : 11.07 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.24), residues: 1168 helix: 2.54 (0.27), residues: 373 sheet: 0.06 (0.35), residues: 219 loop : -1.04 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 219 TYR 0.014 0.001 TYR A1050 PHE 0.014 0.001 PHE A1003 TRP 0.011 0.001 TRP A1099 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9455) covalent geometry : angle 0.44899 (12828) hydrogen bonds : bond 0.03789 ( 399) hydrogen bonds : angle 4.29391 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.291 Fit side-chains REVERT: A 182 ASP cc_start: 0.8024 (t0) cc_final: 0.7650 (t0) REVERT: A 207 ASP cc_start: 0.7738 (t0) cc_final: 0.7452 (t70) REVERT: A 283 ASP cc_start: 0.8658 (t70) cc_final: 0.8372 (t0) REVERT: A 651 MET cc_start: 0.0194 (mpp) cc_final: -0.0312 (tpt) REVERT: A 763 ASP cc_start: 0.7894 (m-30) cc_final: 0.7133 (m-30) REVERT: A 872 SER cc_start: 0.9026 (t) cc_final: 0.8729 (p) REVERT: A 1005 THR cc_start: 0.9090 (m) cc_final: 0.8743 (p) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 0.1087 time to fit residues: 16.5979 Evaluate side-chains 111 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1058 ASP Chi-restraints excluded: chain A residue 1117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.187232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.127819 restraints weight = 10283.020| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.85 r_work: 0.2992 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9455 Z= 0.101 Angle : 0.447 5.508 12828 Z= 0.238 Chirality : 0.042 0.237 1464 Planarity : 0.003 0.049 1674 Dihedral : 4.052 13.476 1298 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.15 % Allowed : 11.36 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1168 helix: 2.61 (0.27), residues: 373 sheet: 0.12 (0.35), residues: 219 loop : -0.98 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 219 TYR 0.014 0.001 TYR A1050 PHE 0.015 0.001 PHE A1003 TRP 0.010 0.001 TRP A1099 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9455) covalent geometry : angle 0.44704 (12828) hydrogen bonds : bond 0.03726 ( 399) hydrogen bonds : angle 4.22405 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.330 Fit side-chains REVERT: A 182 ASP cc_start: 0.8030 (t0) cc_final: 0.7664 (t0) REVERT: A 207 ASP cc_start: 0.7700 (t0) cc_final: 0.7434 (t0) REVERT: A 219 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7382 (mmt180) REVERT: A 283 ASP cc_start: 0.8660 (t70) cc_final: 0.8409 (t0) REVERT: A 651 MET cc_start: 0.0131 (mpp) cc_final: -0.0382 (tpt) REVERT: A 763 ASP cc_start: 0.7940 (m-30) cc_final: 0.7200 (m-30) REVERT: A 768 GLU cc_start: 0.8371 (tp30) cc_final: 0.6896 (mt-10) REVERT: A 872 SER cc_start: 0.9052 (t) cc_final: 0.8752 (p) REVERT: A 1005 THR cc_start: 0.9088 (m) cc_final: 0.8750 (p) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.1058 time to fit residues: 15.7054 Evaluate side-chains 111 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1058 ASP Chi-restraints excluded: chain A residue 1117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 60 optimal weight: 0.0030 chunk 103 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 40 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 438 ASN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN A 767 GLN A 864 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.189973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.129757 restraints weight = 10276.090| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.85 r_work: 0.3020 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9455 Z= 0.080 Angle : 0.428 9.543 12828 Z= 0.226 Chirality : 0.041 0.213 1464 Planarity : 0.003 0.049 1674 Dihedral : 3.806 13.215 1298 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.06 % Allowed : 11.74 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1168 helix: 2.78 (0.27), residues: 373 sheet: -0.06 (0.34), residues: 238 loop : -0.74 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.013 0.001 TYR A1050 PHE 0.013 0.001 PHE A 128 TRP 0.008 0.001 TRP A1099 HIS 0.003 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 9455) covalent geometry : angle 0.42785 (12828) hydrogen bonds : bond 0.03250 ( 399) hydrogen bonds : angle 4.06315 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.339 Fit side-chains REVERT: A 182 ASP cc_start: 0.7965 (t0) cc_final: 0.7597 (t0) REVERT: A 219 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7468 (mmt180) REVERT: A 283 ASP cc_start: 0.8685 (t70) cc_final: 0.8419 (t0) REVERT: A 651 MET cc_start: 0.0219 (mpp) cc_final: -0.0432 (tpt) REVERT: A 872 SER cc_start: 0.8969 (t) cc_final: 0.8727 (p) REVERT: A 1005 THR cc_start: 0.9041 (m) cc_final: 0.8763 (p) outliers start: 11 outliers final: 5 residues processed: 120 average time/residue: 0.1006 time to fit residues: 16.5764 Evaluate side-chains 112 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 9 optimal weight: 0.1980 chunk 109 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** 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 = 0.3968 r_free = 0.3968 target = 0.190313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.130316 restraints weight = 10368.354| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.92 r_work: 0.3026 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9455 Z= 0.080 Angle : 0.430 10.970 12828 Z= 0.226 Chirality : 0.041 0.208 1464 Planarity : 0.003 0.049 1674 Dihedral : 3.710 13.289 1298 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.77 % Allowed : 12.32 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.25), residues: 1168 helix: 2.78 (0.27), residues: 376 sheet: 0.01 (0.34), residues: 238 loop : -0.67 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.013 0.001 TYR A1050 PHE 0.013 0.001 PHE A1003 TRP 0.010 0.001 TRP A1099 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 9455) covalent geometry : angle 0.42975 (12828) hydrogen bonds : bond 0.03196 ( 399) hydrogen bonds : angle 4.00536 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.333 Fit side-chains REVERT: A 89 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 182 ASP cc_start: 0.7912 (t0) cc_final: 0.7574 (t0) REVERT: A 219 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7506 (mmt180) REVERT: A 651 MET cc_start: 0.0163 (mpp) cc_final: -0.0464 (tpt) REVERT: A 768 GLU cc_start: 0.8368 (tp30) cc_final: 0.6757 (mt-10) REVERT: A 872 SER cc_start: 0.8949 (t) cc_final: 0.8717 (p) REVERT: A 1005 THR cc_start: 0.9055 (m) cc_final: 0.8784 (p) outliers start: 8 outliers final: 6 residues processed: 111 average time/residue: 0.1068 time to fit residues: 16.2956 Evaluate side-chains 112 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 95 optimal weight: 0.0980 chunk 49 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.186563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.125591 restraints weight = 10255.484| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.81 r_work: 0.2972 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9455 Z= 0.132 Angle : 0.481 10.875 12828 Z= 0.252 Chirality : 0.043 0.206 1464 Planarity : 0.004 0.049 1674 Dihedral : 3.996 13.862 1298 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.77 % Allowed : 12.51 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1168 helix: 2.54 (0.27), residues: 377 sheet: 0.07 (0.33), residues: 242 loop : -0.78 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.013 0.001 TYR A1125 PHE 0.016 0.001 PHE A1003 TRP 0.011 0.001 TRP A1099 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9455) covalent geometry : angle 0.48104 (12828) hydrogen bonds : bond 0.04107 ( 399) hydrogen bonds : angle 4.20619 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2737.34 seconds wall clock time: 47 minutes 24.07 seconds (2844.07 seconds total)