Starting phenix.real_space_refine on Thu Feb 13 21:00:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whn_32505/02_2025/7whn_32505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whn_32505/02_2025/7whn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7whn_32505/02_2025/7whn_32505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whn_32505/02_2025/7whn_32505.map" model { file = "/net/cci-nas-00/data/ceres_data/7whn_32505/02_2025/7whn_32505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whn_32505/02_2025/7whn_32505.cif" } resolution = 3.3 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= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.73, per 1000 atoms: 0.62 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.99 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: 3.27 Time building geometry restraints manager: 2.59 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.670 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- 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= 0.577 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 (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: -1.29 (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 TRP 0.017 0.002 TRP A1099 HIS 0.007 0.002 HIS A 317 PHE 0.027 0.003 PHE A1140 TYR 0.031 0.003 TYR A 234 ARG 0.014 0.001 ARG A 219 *********************** 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 : 1.060 Fit side-chains REVERT: A 182 ASP cc_start: 0.8279 (t0) cc_final: 0.7943 (t0) REVERT: A 763 ASP cc_start: 0.7673 (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: 0.2896 time to fit residues: 40.1370 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 : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.185638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.125446 restraints weight = 10194.077| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.79 r_work: 0.2975 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1052 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= 0.189 Angle : 0.522 5.910 12828 Z= 0.283 Chirality : 0.044 0.148 1464 Planarity : 0.004 0.063 1674 Dihedral : 4.889 17.811 1298 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.29 % Allowed : 5.20 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.46 (0.24), residues: 1168 helix: 1.56 (0.27), residues: 377 sheet: -0.36 (0.34), residues: 210 loop : -1.60 (0.22), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1099 HIS 0.003 0.001 HIS A 317 PHE 0.014 0.001 PHE A 128 TYR 0.016 0.001 TYR A1050 ARG 0.004 0.000 ARG A 381 *********************** 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 116 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.994 Fit side-chains REVERT: A 182 ASP cc_start: 0.8205 (t0) cc_final: 0.7983 (t70) REVERT: A 282 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7933 (mm-30) REVERT: A 763 ASP cc_start: 0.8036 (m-30) cc_final: 0.7249 (m-30) REVERT: A 872 SER cc_start: 0.9038 (t) cc_final: 0.8678 (p) outliers start: 3 outliers final: 3 residues processed: 113 average time/residue: 0.2578 time to fit residues: 39.6828 Evaluate side-chains 107 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 934 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 993 ASN A1139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.184993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.124329 restraints weight = 10348.761| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.87 r_work: 0.2960 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1324 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= 0.217 Angle : 0.503 5.614 12828 Z= 0.271 Chirality : 0.043 0.144 1464 Planarity : 0.004 0.056 1674 Dihedral : 4.610 16.691 1298 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.96 % Allowed : 7.41 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.16 (0.24), residues: 1168 helix: 1.71 (0.27), residues: 388 sheet: -0.18 (0.32), residues: 237 loop : -1.46 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1099 HIS 0.004 0.001 HIS A 317 PHE 0.016 0.001 PHE A1003 TYR 0.014 0.001 TYR A1050 ARG 0.004 0.000 ARG A 219 *********************** 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 119 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.936 Fit side-chains REVERT: A 182 ASP cc_start: 0.8127 (t0) cc_final: 0.7801 (t0) REVERT: A 207 ASP cc_start: 0.7830 (t0) cc_final: 0.7517 (t70) REVERT: A 282 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8053 (mm-30) REVERT: A 651 MET cc_start: 0.0847 (mpp) cc_final: -0.0136 (tpt) REVERT: A 763 ASP cc_start: 0.8017 (m-30) cc_final: 0.7165 (m-30) REVERT: A 872 SER cc_start: 0.9031 (t) cc_final: 0.8657 (p) outliers start: 10 outliers final: 6 residues processed: 113 average time/residue: 0.2448 time to fit residues: 37.6067 Evaluate side-chains 113 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 367 MET Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1122 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.183519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.124163 restraints weight = 10290.205| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.77 r_work: 0.2955 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9455 Z= 0.282 Angle : 0.522 5.705 12828 Z= 0.280 Chirality : 0.044 0.145 1464 Planarity : 0.004 0.054 1674 Dihedral : 4.646 15.673 1298 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.54 % Allowed : 9.14 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.12 (0.24), residues: 1168 helix: 1.76 (0.27), residues: 383 sheet: -0.10 (0.33), residues: 220 loop : -1.42 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1099 HIS 0.006 0.001 HIS A 307 PHE 0.017 0.002 PHE A1003 TYR 0.015 0.002 TYR A 234 ARG 0.004 0.000 ARG A 219 *********************** 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 126 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.062 Fit side-chains REVERT: A 182 ASP cc_start: 0.8139 (t0) cc_final: 0.7715 (t0) REVERT: A 569 MET cc_start: 0.1809 (mtt) cc_final: 0.1542 (mtt) REVERT: A 651 MET cc_start: 0.0514 (mpp) cc_final: -0.0369 (tpt) REVERT: A 763 ASP cc_start: 0.8002 (m-30) cc_final: 0.7192 (m-30) REVERT: A 866 SER cc_start: 0.8555 (t) cc_final: 0.8328 (m) REVERT: A 872 SER cc_start: 0.9092 (t) cc_final: 0.8682 (p) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.2639 time to fit residues: 42.6786 Evaluate side-chains 118 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 367 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1122 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.183022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.123434 restraints weight = 10310.115| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.76 r_work: 0.2952 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9455 Z= 0.296 Angle : 0.524 5.720 12828 Z= 0.281 Chirality : 0.045 0.145 1464 Planarity : 0.004 0.053 1674 Dihedral : 4.633 16.136 1298 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.83 % Allowed : 10.11 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.09 (0.24), residues: 1168 helix: 1.78 (0.27), residues: 382 sheet: -0.05 (0.34), residues: 220 loop : -1.40 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1099 HIS 0.006 0.001 HIS A 317 PHE 0.017 0.002 PHE A1003 TYR 0.015 0.002 TYR A1125 ARG 0.005 0.000 ARG A 219 *********************** 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 131 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.019 Fit side-chains REVERT: A 89 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8167 (mt-10) REVERT: A 182 ASP cc_start: 0.8146 (t0) cc_final: 0.7686 (t0) REVERT: A 651 MET cc_start: 0.0390 (mpp) cc_final: -0.0349 (tpt) REVERT: A 754 HIS cc_start: 0.9013 (OUTLIER) cc_final: 0.8259 (p90) REVERT: A 763 ASP cc_start: 0.7965 (m-30) cc_final: 0.7184 (m-30) REVERT: A 866 SER cc_start: 0.8523 (t) cc_final: 0.8297 (m) REVERT: A 872 SER cc_start: 0.9055 (t) cc_final: 0.8644 (p) outliers start: 19 outliers final: 8 residues processed: 121 average time/residue: 0.2481 time to fit residues: 41.0374 Evaluate side-chains 117 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 315 MET Chi-restraints excluded: chain A residue 367 MET 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 1117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN A1053 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.185482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.125761 restraints weight = 10259.006| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.79 r_work: 0.2980 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9455 Z= 0.179 Angle : 0.464 5.557 12828 Z= 0.249 Chirality : 0.042 0.142 1464 Planarity : 0.004 0.051 1674 Dihedral : 4.320 14.322 1298 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.54 % Allowed : 10.88 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.21 (0.24), residues: 1168 helix: 2.06 (0.27), residues: 386 sheet: -0.12 (0.33), residues: 233 loop : -1.18 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1099 HIS 0.004 0.001 HIS A 317 PHE 0.015 0.001 PHE A1003 TYR 0.014 0.001 TYR A1050 ARG 0.005 0.000 ARG A 219 *********************** 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 128 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.967 Fit side-chains REVERT: A 89 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 182 ASP cc_start: 0.8092 (t0) cc_final: 0.7719 (t0) REVERT: A 283 ASP cc_start: 0.8663 (t70) cc_final: 0.8160 (t0) REVERT: A 651 MET cc_start: 0.0104 (mpp) cc_final: -0.0340 (tpt) REVERT: A 754 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8224 (p90) REVERT: A 763 ASP cc_start: 0.7966 (m-30) cc_final: 0.7190 (m-30) REVERT: A 872 SER cc_start: 0.9019 (t) cc_final: 0.8688 (p) REVERT: A 1005 THR cc_start: 0.9095 (m) cc_final: 0.8733 (p) REVERT: A 1039 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7912 (mtpt) outliers start: 16 outliers final: 10 residues processed: 119 average time/residue: 0.2531 time to fit residues: 40.8442 Evaluate side-chains 122 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 315 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 934 ASP 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 68 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 40.0000 chunk 98 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.184559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.125097 restraints weight = 10372.512| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.82 r_work: 0.2969 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9455 Z= 0.219 Angle : 0.485 5.984 12828 Z= 0.258 Chirality : 0.044 0.272 1464 Planarity : 0.004 0.050 1674 Dihedral : 4.331 14.345 1298 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.64 % Allowed : 11.36 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.33 (0.24), residues: 1168 helix: 2.28 (0.27), residues: 374 sheet: -0.05 (0.35), residues: 218 loop : -1.11 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1099 HIS 0.005 0.001 HIS A 317 PHE 0.016 0.001 PHE A1003 TYR 0.013 0.001 TYR A1050 ARG 0.006 0.000 ARG A 219 *********************** 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 127 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.122 Fit side-chains REVERT: A 89 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 182 ASP cc_start: 0.8110 (t0) cc_final: 0.7729 (t0) REVERT: A 283 ASP cc_start: 0.8650 (t70) cc_final: 0.8140 (t0) REVERT: A 651 MET cc_start: 0.0074 (mpp) cc_final: -0.0372 (tpt) REVERT: A 754 HIS cc_start: 0.8994 (OUTLIER) cc_final: 0.8251 (p90) REVERT: A 763 ASP cc_start: 0.7994 (m-30) cc_final: 0.7224 (m-30) REVERT: A 866 SER cc_start: 0.8496 (t) cc_final: 0.8279 (m) REVERT: A 872 SER cc_start: 0.9079 (t) cc_final: 0.8700 (p) REVERT: A 1005 THR cc_start: 0.9096 (m) cc_final: 0.8728 (p) REVERT: A 1039 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7983 (mtpt) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.2780 time to fit residues: 44.6083 Evaluate side-chains 122 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 315 MET Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 754 HIS 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 86 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.182304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.123216 restraints weight = 10480.127| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.82 r_work: 0.2938 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9455 Z= 0.356 Angle : 0.554 7.596 12828 Z= 0.295 Chirality : 0.046 0.230 1464 Planarity : 0.004 0.051 1674 Dihedral : 4.654 16.855 1298 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.73 % Allowed : 11.84 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.07 (0.24), residues: 1168 helix: 1.90 (0.27), residues: 380 sheet: -0.04 (0.34), residues: 220 loop : -1.24 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1099 HIS 0.007 0.001 HIS A 317 PHE 0.019 0.002 PHE A1003 TYR 0.017 0.002 TYR A1125 ARG 0.007 0.000 ARG A 219 *********************** 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 127 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.994 Fit side-chains REVERT: A 89 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8111 (mt-10) REVERT: A 182 ASP cc_start: 0.8168 (t0) cc_final: 0.7734 (t0) REVERT: A 207 ASP cc_start: 0.7843 (t0) cc_final: 0.7561 (t0) REVERT: A 651 MET cc_start: 0.0137 (mpp) cc_final: -0.0330 (tpt) REVERT: A 672 MET cc_start: 0.1199 (mmt) cc_final: 0.0676 (ptm) REVERT: A 754 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.8294 (p90) REVERT: A 763 ASP cc_start: 0.8001 (m-30) cc_final: 0.7182 (m-30) REVERT: A 866 SER cc_start: 0.8608 (t) cc_final: 0.8358 (m) REVERT: A 872 SER cc_start: 0.9124 (t) cc_final: 0.8673 (p) outliers start: 18 outliers final: 12 residues processed: 117 average time/residue: 0.2616 time to fit residues: 41.4623 Evaluate side-chains 123 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 315 MET Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 1058 ASP Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1153 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 46 optimal weight: 0.0020 chunk 110 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN A 767 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.187402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.126878 restraints weight = 10223.158| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.78 r_work: 0.2992 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2016 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= 0.123 Angle : 0.444 5.478 12828 Z= 0.238 Chirality : 0.042 0.220 1464 Planarity : 0.004 0.049 1674 Dihedral : 4.117 14.178 1298 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.15 % Allowed : 12.51 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.57 (0.25), residues: 1168 helix: 2.54 (0.27), residues: 373 sheet: 0.01 (0.34), residues: 234 loop : -0.98 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1099 HIS 0.003 0.001 HIS A 317 PHE 0.014 0.001 PHE A 128 TYR 0.013 0.001 TYR A1050 ARG 0.007 0.000 ARG A 219 *********************** 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 120 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.108 Fit side-chains REVERT: A 89 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8198 (mt-10) REVERT: A 182 ASP cc_start: 0.8055 (t0) cc_final: 0.7668 (t0) REVERT: A 207 ASP cc_start: 0.7753 (t0) cc_final: 0.7488 (t0) REVERT: A 219 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7390 (mmt180) REVERT: A 283 ASP cc_start: 0.8622 (t70) cc_final: 0.8323 (t0) REVERT: A 651 MET cc_start: 0.0147 (mpp) cc_final: -0.0389 (tpt) REVERT: A 672 MET cc_start: 0.0747 (mmt) cc_final: 0.0266 (ptm) REVERT: A 754 HIS cc_start: 0.8968 (OUTLIER) cc_final: 0.8261 (p90) REVERT: A 872 SER cc_start: 0.8947 (t) cc_final: 0.8686 (p) REVERT: A 1005 THR cc_start: 0.9093 (m) cc_final: 0.8743 (p) outliers start: 12 outliers final: 8 residues processed: 114 average time/residue: 0.2466 time to fit residues: 38.7833 Evaluate side-chains 112 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 377 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 1058 ASP Chi-restraints excluded: chain A residue 1117 SER 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 46 optimal weight: 0.0070 chunk 22 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 0.0270 chunk 113 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.189678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.130749 restraints weight = 10399.327| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.97 r_work: 0.3033 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2378 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= 0.113 Angle : 0.422 5.544 12828 Z= 0.225 Chirality : 0.041 0.210 1464 Planarity : 0.003 0.049 1674 Dihedral : 3.770 13.432 1298 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.87 % Allowed : 12.90 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.85 (0.25), residues: 1168 helix: 2.79 (0.27), residues: 373 sheet: -0.00 (0.35), residues: 228 loop : -0.74 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1099 HIS 0.003 0.000 HIS A 317 PHE 0.012 0.001 PHE A1003 TYR 0.011 0.001 TYR A1050 ARG 0.007 0.000 ARG A 219 ********************** 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 122 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.081 Fit side-chains REVERT: A 89 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8200 (mt-10) REVERT: A 182 ASP cc_start: 0.7995 (t0) cc_final: 0.7675 (t0) REVERT: A 207 ASP cc_start: 0.7712 (t0) cc_final: 0.7459 (t0) REVERT: A 219 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7420 (mmt180) REVERT: A 283 ASP cc_start: 0.8618 (t70) cc_final: 0.8309 (t0) REVERT: A 651 MET cc_start: -0.0141 (mpp) cc_final: -0.0592 (tpt) REVERT: A 672 MET cc_start: 0.0508 (mmt) cc_final: 0.0246 (ptm) REVERT: A 754 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8225 (p90) REVERT: A 872 SER cc_start: 0.8940 (t) cc_final: 0.8716 (p) REVERT: A 1005 THR cc_start: 0.9114 (m) cc_final: 0.8784 (p) outliers start: 9 outliers final: 5 residues processed: 118 average time/residue: 0.2326 time to fit residues: 37.9846 Evaluate side-chains 111 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 1058 ASP 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 26 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.188077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.127909 restraints weight = 10384.831| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.91 r_work: 0.3001 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9455 Z= 0.148 Angle : 0.439 5.592 12828 Z= 0.233 Chirality : 0.042 0.204 1464 Planarity : 0.004 0.050 1674 Dihedral : 3.828 14.162 1298 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.87 % Allowed : 12.99 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.84 (0.25), residues: 1168 helix: 2.71 (0.27), residues: 376 sheet: 0.01 (0.35), residues: 228 loop : -0.71 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1099 HIS 0.003 0.001 HIS A 317 PHE 0.014 0.001 PHE A1003 TYR 0.011 0.001 TYR A1125 ARG 0.006 0.000 ARG A 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5492.08 seconds wall clock time: 97 minutes 49.96 seconds (5869.96 seconds total)