Starting phenix.real_space_refine on Wed Mar 4 01:55:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wuf_66260/03_2026/9wuf_66260_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wuf_66260/03_2026/9wuf_66260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wuf_66260/03_2026/9wuf_66260_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wuf_66260/03_2026/9wuf_66260_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wuf_66260/03_2026/9wuf_66260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wuf_66260/03_2026/9wuf_66260.map" } resolution = 3.01 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= 0.001 sd= 0.021 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 44 5.16 5 C 6083 2.51 5 N 1668 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 9585 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1212, 9585 Classifications: {'peptide': 1212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1163} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.40, per 1000 atoms: 0.25 Number of scatterers: 9585 At special positions: 0 Unit cell: (85.808, 91.344, 132.172, 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 44 16.00 O 1790 8.00 N 1668 7.00 C 6083 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: 0.81 Conformation dependent library (CDL) restraints added in 550.2 milliseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 54.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.572A pdb=" N LYS A 35 " --> pdb=" O ASP A 31 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 48 through 60 removed outlier: 3.776A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 removed outlier: 6.160A pdb=" N ALA A 64 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 66 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N SER A 67 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 83 Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 137 through 152 removed outlier: 3.566A pdb=" N TYR A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 179 removed outlier: 3.985A pdb=" N LEU A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 removed outlier: 3.759A pdb=" N ARG A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 268 through 284 removed outlier: 3.593A pdb=" N ARG A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 305 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 385 Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 435 through 451 removed outlier: 3.543A pdb=" N GLN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 472 removed outlier: 4.016A pdb=" N ASN A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.920A pdb=" N ILE A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 578 through 604 removed outlier: 4.348A pdb=" N GLY A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG A 595 " --> pdb=" O THR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 628 removed outlier: 3.771A pdb=" N PHE A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 638 Processing helix chain 'A' and resid 657 through 665 removed outlier: 4.465A pdb=" N LEU A 660 " --> pdb=" O ASP A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.904A pdb=" N LEU A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 703 Processing helix chain 'A' and resid 718 through 722 Processing helix chain 'A' and resid 723 through 727 Processing helix chain 'A' and resid 735 through 751 Processing helix chain 'A' and resid 761 through 785 Processing helix chain 'A' and resid 788 through 821 removed outlier: 4.395A pdb=" N ALA A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 856 removed outlier: 4.308A pdb=" N CYS A 854 " --> pdb=" O GLU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 891 Processing helix chain 'A' and resid 932 through 936 Processing helix chain 'A' and resid 965 through 977 Processing helix chain 'A' and resid 979 through 998 Processing helix chain 'A' and resid 1006 through 1016 Processing helix chain 'A' and resid 1019 through 1030 Processing helix chain 'A' and resid 1046 through 1050 Processing helix chain 'A' and resid 1080 through 1098 Processing helix chain 'A' and resid 1101 through 1105 removed outlier: 3.527A pdb=" N PHE A1105 " --> pdb=" O ARG A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1112 Processing helix chain 'A' and resid 1124 through 1135 removed outlier: 3.549A pdb=" N ILE A1135 " --> pdb=" O GLU A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.902A pdb=" N GLU A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A1195 " --> pdb=" O SER A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1221 Processing helix chain 'A' and resid 1221 through 1230 Processing helix chain 'A' and resid 1265 through 1271 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 123 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 212 Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 322 removed outlier: 5.198A pdb=" N THR A 327 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A 346 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N MET A 329 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE A 344 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE A 333 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET A 340 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 457 removed outlier: 3.715A pdb=" N LEU A 495 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 515 through 519 removed outlier: 5.123A pdb=" N THR A 558 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 758 through 760 removed outlier: 7.092A pdb=" N ASP A 897 " --> pdb=" O ARG A 909 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 909 " --> pdb=" O ASP A 897 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1002 through 1005 Processing sheet with id=AA8, first strand: chain 'A' and resid 1138 through 1144 removed outlier: 6.702A pdb=" N ASP A1161 " --> pdb=" O GLY A1142 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY A1144 " --> pdb=" O ASP A1159 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP A1159 " --> pdb=" O GLY A1144 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N ILE A1160 " --> pdb=" O CYS A1177 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N CYS A1177 " --> pdb=" O ILE A1160 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N ASN A1262 " --> pdb=" O ILE A1236 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER A1238 " --> pdb=" O ASN A1262 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY A1264 " --> pdb=" O SER A1238 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A1240 " --> pdb=" O GLY A1264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1200 through 1201 518 hydrogen bonds defined for protein. 1464 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: 2.13 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3234 1.34 - 1.46: 2159 1.46 - 1.58: 4302 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 9772 Sorted by residual: bond pdb=" C GLU A 690 " pdb=" O GLU A 690 " ideal model delta sigma weight residual 1.234 1.241 -0.007 5.00e-03 4.00e+04 1.91e+00 bond pdb=" CA ASP A 473 " pdb=" CB ASP A 473 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.38e+00 bond pdb=" CB ASP A 774 " pdb=" CG ASP A 774 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CA GLU A 286 " pdb=" C GLU A 286 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.56e-02 4.11e+03 1.15e+00 bond pdb=" CB MET A 867 " pdb=" CG MET A 867 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.08e+00 ... (remaining 9767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 12996 2.20 - 4.40: 195 4.40 - 6.61: 33 6.61 - 8.81: 3 8.81 - 11.01: 2 Bond angle restraints: 13229 Sorted by residual: angle pdb=" CB MET A 496 " pdb=" CG MET A 496 " pdb=" SD MET A 496 " ideal model delta sigma weight residual 112.70 123.71 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CA GLU A 998 " pdb=" CB GLU A 998 " pdb=" CG GLU A 998 " ideal model delta sigma weight residual 114.10 121.28 -7.18 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CB MET A 636 " pdb=" CG MET A 636 " pdb=" SD MET A 636 " ideal model delta sigma weight residual 112.70 123.28 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C ASP A 115 " pdb=" N VAL A 116 " pdb=" CA VAL A 116 " ideal model delta sigma weight residual 120.35 125.15 -4.80 1.39e+00 5.18e-01 1.19e+01 angle pdb=" C GLY A1144 " pdb=" N PHE A1145 " pdb=" CA PHE A1145 " ideal model delta sigma weight residual 120.06 123.96 -3.90 1.19e+00 7.06e-01 1.07e+01 ... (remaining 13224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5334 17.79 - 35.57: 453 35.57 - 53.36: 87 53.36 - 71.15: 22 71.15 - 88.93: 5 Dihedral angle restraints: 5901 sinusoidal: 2408 harmonic: 3493 Sorted by residual: dihedral pdb=" CA SER A 922 " pdb=" C SER A 922 " pdb=" N LYS A 923 " pdb=" CA LYS A 923 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA HIS A 712 " pdb=" C HIS A 712 " pdb=" N ILE A 713 " pdb=" CA ILE A 713 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA THR A1138 " pdb=" C THR A1138 " pdb=" N VAL A1139 " pdb=" CA VAL A1139 " ideal model delta harmonic sigma weight residual 180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1022 0.036 - 0.071: 333 0.071 - 0.107: 93 0.107 - 0.142: 28 0.142 - 0.178: 4 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CA ASP A 473 " pdb=" N ASP A 473 " pdb=" C ASP A 473 " pdb=" CB ASP A 473 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB ILE A 333 " pdb=" CA ILE A 333 " pdb=" CG1 ILE A 333 " pdb=" CG2 ILE A 333 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA ILE A 651 " pdb=" N ILE A 651 " pdb=" C ILE A 651 " pdb=" CB ILE A 651 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 1477 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 79 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C ALA A 79 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA A 79 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 80 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 998 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.44e+00 pdb=" C GLU A 998 " 0.032 2.00e-02 2.50e+03 pdb=" O GLU A 998 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 999 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 74 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C LEU A 74 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 74 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 75 " -0.009 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 643 2.73 - 3.27: 10533 3.27 - 3.82: 16642 3.82 - 4.36: 20009 4.36 - 4.90: 33540 Nonbonded interactions: 81367 Sorted by model distance: nonbonded pdb=" OH TYR A 298 " pdb=" O GLY A 399 " model vdw 2.189 3.040 nonbonded pdb=" NZ LYS A 323 " pdb=" OD2 ASP A 364 " model vdw 2.222 3.120 nonbonded pdb=" OD2 ASP A 291 " pdb=" OG SER A 348 " model vdw 2.244 3.040 nonbonded pdb=" OE1 GLN A 242 " pdb=" N VAL A 243 " model vdw 2.252 3.120 nonbonded pdb=" N GLU A 250 " pdb=" OE1 GLU A 250 " model vdw 2.252 3.120 ... (remaining 81362 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: 3.900 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.003 0.031 9772 Z= 0.164 Angle : 0.690 11.010 13229 Z= 0.374 Chirality : 0.041 0.178 1480 Planarity : 0.004 0.037 1722 Dihedral : 14.031 88.931 3641 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.40 % Favored : 96.35 % Rotamer: Outliers : 0.10 % Allowed : 11.80 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.24), residues: 1206 helix: 0.75 (0.21), residues: 573 sheet: -1.10 (0.47), residues: 122 loop : -0.39 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1005 TYR 0.011 0.001 TYR A 659 PHE 0.018 0.002 PHE A1228 TRP 0.014 0.001 TRP A 440 HIS 0.006 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9772) covalent geometry : angle 0.68997 (13229) hydrogen bonds : bond 0.15447 ( 518) hydrogen bonds : angle 6.57044 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.346 Fit side-chains REVERT: A 238 MET cc_start: 0.9672 (ptp) cc_final: 0.9375 (ptp) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.0821 time to fit residues: 8.0239 Evaluate side-chains 57 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 821 HIS A1085 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.064534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.049275 restraints weight = 41819.360| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.36 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9772 Z= 0.279 Angle : 0.661 9.748 13229 Z= 0.343 Chirality : 0.043 0.176 1480 Planarity : 0.004 0.040 1722 Dihedral : 4.772 23.858 1324 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 0.88 % Allowed : 11.90 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.24), residues: 1206 helix: 1.11 (0.21), residues: 579 sheet: -1.41 (0.44), residues: 126 loop : -0.51 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 590 TYR 0.019 0.002 TYR A 128 PHE 0.017 0.002 PHE A 537 TRP 0.015 0.002 TRP A 419 HIS 0.004 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 9772) covalent geometry : angle 0.66108 (13229) hydrogen bonds : bond 0.05010 ( 518) hydrogen bonds : angle 5.08076 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.386 Fit side-chains REVERT: A 217 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8289 (tpp80) REVERT: A 246 GLU cc_start: 0.7147 (mp0) cc_final: 0.6647 (mp0) REVERT: A 298 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: A 529 MET cc_start: 0.8534 (ppp) cc_final: 0.8187 (ppp) REVERT: A 655 LEU cc_start: 0.8671 (mt) cc_final: 0.8464 (mt) outliers start: 9 outliers final: 5 residues processed: 69 average time/residue: 0.0949 time to fit residues: 9.7588 Evaluate side-chains 63 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 456 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 60 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 500 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 = 0.3655 r_free = 0.3655 target = 0.066465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.051551 restraints weight = 42203.073| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 4.45 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9772 Z= 0.123 Angle : 0.544 7.055 13229 Z= 0.280 Chirality : 0.040 0.167 1480 Planarity : 0.004 0.041 1722 Dihedral : 4.348 20.992 1324 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 1.46 % Allowed : 11.90 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.24), residues: 1206 helix: 1.58 (0.21), residues: 582 sheet: -0.99 (0.46), residues: 128 loop : -0.34 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.012 0.001 TYR A 659 PHE 0.013 0.001 PHE A 627 TRP 0.010 0.001 TRP A 468 HIS 0.002 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9772) covalent geometry : angle 0.54403 (13229) hydrogen bonds : bond 0.03886 ( 518) hydrogen bonds : angle 4.62710 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.9541 (ptp) cc_final: 0.9154 (mpp) REVERT: A 298 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: A 529 MET cc_start: 0.8514 (ppp) cc_final: 0.8259 (ppp) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.0760 time to fit residues: 10.1787 Evaluate side-chains 73 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 1113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.064014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.048778 restraints weight = 42260.980| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.46 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9772 Z= 0.288 Angle : 0.643 7.067 13229 Z= 0.329 Chirality : 0.042 0.159 1480 Planarity : 0.004 0.039 1722 Dihedral : 4.487 21.445 1324 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 2.24 % Allowed : 13.07 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.24), residues: 1206 helix: 1.42 (0.21), residues: 585 sheet: -1.19 (0.45), residues: 126 loop : -0.50 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 590 TYR 0.033 0.002 TYR A 128 PHE 0.016 0.002 PHE A 537 TRP 0.012 0.002 TRP A1038 HIS 0.003 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 9772) covalent geometry : angle 0.64333 (13229) hydrogen bonds : bond 0.04429 ( 518) hydrogen bonds : angle 4.83010 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 248 MET cc_start: 0.8215 (tpp) cc_final: 0.8010 (tpt) REVERT: A 298 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: A 529 MET cc_start: 0.8552 (ppp) cc_final: 0.8247 (ppp) REVERT: A 580 MET cc_start: 0.8763 (mmp) cc_final: 0.8259 (tmm) REVERT: A 636 MET cc_start: 0.8218 (tpp) cc_final: 0.7863 (tpp) REVERT: A 1004 MET cc_start: 0.8136 (ptm) cc_final: 0.7895 (ptm) outliers start: 23 outliers final: 9 residues processed: 80 average time/residue: 0.0882 time to fit residues: 10.3404 Evaluate side-chains 68 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 865 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 389 GLN A 500 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.066765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.051741 restraints weight = 41367.035| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.55 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9772 Z= 0.111 Angle : 0.538 7.516 13229 Z= 0.274 Chirality : 0.040 0.224 1480 Planarity : 0.003 0.039 1722 Dihedral : 4.206 20.336 1324 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 1.66 % Allowed : 14.73 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.25), residues: 1206 helix: 1.74 (0.21), residues: 583 sheet: -0.97 (0.45), residues: 128 loop : -0.38 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1133 TYR 0.019 0.001 TYR A 128 PHE 0.011 0.001 PHE A 537 TRP 0.010 0.001 TRP A 468 HIS 0.002 0.001 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9772) covalent geometry : angle 0.53775 (13229) hydrogen bonds : bond 0.03553 ( 518) hydrogen bonds : angle 4.53312 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 298 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8450 (m-80) REVERT: A 529 MET cc_start: 0.8567 (ppp) cc_final: 0.8217 (ppp) outliers start: 17 outliers final: 9 residues processed: 79 average time/residue: 0.0761 time to fit residues: 9.1225 Evaluate side-chains 70 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 1113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 7 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 79 optimal weight: 0.0670 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.066312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.051215 restraints weight = 41838.956| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.55 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9772 Z= 0.138 Angle : 0.549 8.362 13229 Z= 0.276 Chirality : 0.039 0.169 1480 Planarity : 0.003 0.036 1722 Dihedral : 4.112 20.048 1324 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 1.85 % Allowed : 14.83 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.25), residues: 1206 helix: 1.77 (0.21), residues: 586 sheet: -0.98 (0.45), residues: 128 loop : -0.37 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1133 TYR 0.017 0.001 TYR A 128 PHE 0.010 0.001 PHE A 537 TRP 0.011 0.001 TRP A 468 HIS 0.002 0.000 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9772) covalent geometry : angle 0.54900 (13229) hydrogen bonds : bond 0.03569 ( 518) hydrogen bonds : angle 4.49909 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 87 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8997 (tm-30) REVERT: A 298 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: A 529 MET cc_start: 0.8560 (ppp) cc_final: 0.8201 (ppp) REVERT: A 580 MET cc_start: 0.8776 (mmp) cc_final: 0.8257 (tmm) REVERT: A 1004 MET cc_start: 0.8144 (ptm) cc_final: 0.7473 (ppp) outliers start: 19 outliers final: 11 residues processed: 77 average time/residue: 0.0783 time to fit residues: 9.0954 Evaluate side-chains 71 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.066428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.051298 restraints weight = 41661.447| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.55 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9772 Z= 0.131 Angle : 0.540 9.320 13229 Z= 0.271 Chirality : 0.039 0.159 1480 Planarity : 0.003 0.035 1722 Dihedral : 4.028 20.575 1324 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 1.56 % Allowed : 14.73 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.25), residues: 1206 helix: 1.77 (0.21), residues: 593 sheet: -0.98 (0.44), residues: 135 loop : -0.48 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 626 TYR 0.016 0.001 TYR A 128 PHE 0.010 0.001 PHE A 537 TRP 0.011 0.001 TRP A 468 HIS 0.002 0.000 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9772) covalent geometry : angle 0.53979 (13229) hydrogen bonds : bond 0.03457 ( 518) hydrogen bonds : angle 4.44410 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 87 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.9018 (tm-30) REVERT: A 298 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: A 529 MET cc_start: 0.8549 (ppp) cc_final: 0.8008 (ppp) REVERT: A 1004 MET cc_start: 0.8153 (ptm) cc_final: 0.7488 (ppp) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.0846 time to fit residues: 9.5849 Evaluate side-chains 70 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.067119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052033 restraints weight = 41267.354| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.54 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9772 Z= 0.111 Angle : 0.542 9.902 13229 Z= 0.270 Chirality : 0.039 0.180 1480 Planarity : 0.003 0.034 1722 Dihedral : 3.956 20.952 1324 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.17 % Allowed : 15.22 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.25), residues: 1206 helix: 1.80 (0.21), residues: 594 sheet: -0.91 (0.44), residues: 135 loop : -0.49 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 644 TYR 0.013 0.001 TYR A 128 PHE 0.008 0.001 PHE A 537 TRP 0.011 0.001 TRP A 468 HIS 0.003 0.000 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9772) covalent geometry : angle 0.54208 (13229) hydrogen bonds : bond 0.03357 ( 518) hydrogen bonds : angle 4.41057 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 87 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.9015 (tm-30) REVERT: A 298 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: A 529 MET cc_start: 0.8534 (ppp) cc_final: 0.7997 (ppp) REVERT: A 580 MET cc_start: 0.8791 (mmp) cc_final: 0.8202 (tmm) REVERT: A 1004 MET cc_start: 0.8107 (ptm) cc_final: 0.7450 (ppp) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.0784 time to fit residues: 8.2752 Evaluate side-chains 69 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 89 optimal weight: 0.0980 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.067293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.052208 restraints weight = 41278.201| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 4.50 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9772 Z= 0.109 Angle : 0.535 10.311 13229 Z= 0.265 Chirality : 0.039 0.168 1480 Planarity : 0.003 0.034 1722 Dihedral : 3.888 19.813 1324 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.07 % Allowed : 15.61 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.25), residues: 1206 helix: 1.78 (0.21), residues: 600 sheet: -0.77 (0.45), residues: 130 loop : -0.55 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 644 TYR 0.012 0.001 TYR A 128 PHE 0.008 0.001 PHE A1002 TRP 0.011 0.001 TRP A 468 HIS 0.002 0.000 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9772) covalent geometry : angle 0.53459 (13229) hydrogen bonds : bond 0.03243 ( 518) hydrogen bonds : angle 4.33865 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 87 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.9034 (tm-30) REVERT: A 248 MET cc_start: 0.8445 (tpt) cc_final: 0.8179 (tpt) REVERT: A 298 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: A 529 MET cc_start: 0.8522 (ppp) cc_final: 0.8004 (ppp) REVERT: A 1004 MET cc_start: 0.8083 (ptm) cc_final: 0.7446 (ppp) outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 0.0839 time to fit residues: 8.6538 Evaluate side-chains 66 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 110 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.066431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.051103 restraints weight = 41449.164| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.58 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9772 Z= 0.161 Angle : 0.566 10.528 13229 Z= 0.280 Chirality : 0.040 0.171 1480 Planarity : 0.003 0.033 1722 Dihedral : 3.942 19.274 1324 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.88 % Allowed : 16.29 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.25), residues: 1206 helix: 1.82 (0.21), residues: 594 sheet: -0.94 (0.49), residues: 110 loop : -0.53 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 644 TYR 0.015 0.001 TYR A 128 PHE 0.009 0.001 PHE A 537 TRP 0.011 0.001 TRP A 468 HIS 0.002 0.001 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9772) covalent geometry : angle 0.56576 (13229) hydrogen bonds : bond 0.03505 ( 518) hydrogen bonds : angle 4.41084 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.359 Fit side-chains REVERT: A 87 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.9031 (tm-30) REVERT: A 248 MET cc_start: 0.8450 (tpt) cc_final: 0.8141 (tpt) REVERT: A 298 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: A 529 MET cc_start: 0.8539 (ppp) cc_final: 0.7976 (ppp) REVERT: A 580 MET cc_start: 0.8821 (mmp) cc_final: 0.8187 (tmm) REVERT: A 1004 MET cc_start: 0.8115 (ptm) cc_final: 0.7395 (ppp) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.0828 time to fit residues: 8.3090 Evaluate side-chains 64 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 298 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.067442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.052264 restraints weight = 41215.249| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.54 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9772 Z= 0.110 Angle : 0.550 10.811 13229 Z= 0.271 Chirality : 0.039 0.167 1480 Planarity : 0.003 0.035 1722 Dihedral : 3.875 19.355 1324 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.98 % Allowed : 16.39 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.25), residues: 1206 helix: 1.87 (0.21), residues: 595 sheet: -1.01 (0.45), residues: 129 loop : -0.42 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 644 TYR 0.012 0.001 TYR A 128 PHE 0.008 0.001 PHE A 537 TRP 0.011 0.001 TRP A 468 HIS 0.002 0.000 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9772) covalent geometry : angle 0.55027 (13229) hydrogen bonds : bond 0.03253 ( 518) hydrogen bonds : angle 4.36918 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2057.35 seconds wall clock time: 36 minutes 0.77 seconds (2160.77 seconds total)