Starting phenix.real_space_refine on Wed Mar 12 04:06:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qy7_18747/03_2025/8qy7_18747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qy7_18747/03_2025/8qy7_18747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qy7_18747/03_2025/8qy7_18747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qy7_18747/03_2025/8qy7_18747.map" model { file = "/net/cci-nas-00/data/ceres_data/8qy7_18747/03_2025/8qy7_18747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qy7_18747/03_2025/8qy7_18747.cif" } resolution = 2.66 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= 0.086 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 15 5.16 5 C 4582 2.51 5 N 1241 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7167 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7167 Classifications: {'peptide': 893} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 50, 'TRANS': 842} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.19, per 1000 atoms: 0.72 Number of scatterers: 7167 At special positions: 0 Unit cell: (82.368, 118.144, 95.68, 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 15 16.00 O 1329 8.00 N 1241 7.00 C 4582 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: 1.54 Conformation dependent library (CDL) restraints added in 927.9 milliseconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 9 sheets defined 50.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 147 through 165 Processing helix chain 'A' and resid 169 through 188 Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.613A pdb=" N LYS A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.845A pdb=" N ILE A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.238A pdb=" N PHE A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.808A pdb=" N VAL A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 360 through 377 removed outlier: 3.637A pdb=" N LEU A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'A' and resid 581 through 596 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 641 through 656 Processing helix chain 'A' and resid 657 through 661 removed outlier: 3.908A pdb=" N GLY A 660 " --> pdb=" O TYR A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 3.657A pdb=" N LYS A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 688 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.678A pdb=" N GLN A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 736 removed outlier: 3.589A pdb=" N LYS A 736 " --> pdb=" O GLN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 765 through 777 removed outlier: 4.286A pdb=" N LEU A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 844 through 864 Processing helix chain 'A' and resid 875 through 888 Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.121A pdb=" N VAL A 892 " --> pdb=" O HIS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.803A pdb=" N ARG A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP A 900 " --> pdb=" O PRO A 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 900' Processing helix chain 'A' and resid 902 through 919 Processing helix chain 'A' and resid 929 through 945 Processing helix chain 'A' and resid 959 through 975 Processing helix chain 'A' and resid 1008 through 1017 Processing helix chain 'A' and resid 1042 through 1059 Processing helix chain 'A' and resid 1069 through 1073 Processing helix chain 'A' and resid 1074 through 1079 removed outlier: 4.242A pdb=" N LYS A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A1079 " --> pdb=" O THR A1075 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1074 through 1079' Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 104 removed outlier: 6.222A pdb=" N ARG A 98 " --> pdb=" O TRP A 119 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP A 119 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 100 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 117 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 113 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 133 removed outlier: 3.570A pdb=" N ILE A 136 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 201 removed outlier: 6.537A pdb=" N HIS A 199 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE A 261 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 201 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 214 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.567A pdb=" N ILE A 327 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE A 324 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 663 through 666 removed outlier: 6.442A pdb=" N LEU A 664 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN A 636 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 707 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 638 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 637 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP A 730 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 639 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER A 725 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LEU A 818 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 606 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 832 through 834 removed outlier: 6.540A pdb=" N ILE A 833 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A 998 " --> pdb=" O TYR A1029 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N TYR A1031 " --> pdb=" O ASN A 998 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A1000 " --> pdb=" O TYR A1031 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS A 922 " --> pdb=" O ALA A 997 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A 999 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL A 949 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 841 through 842 removed outlier: 5.963A pdb=" N LEU A 841 " --> pdb=" O ARG A1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 340 hydrogen bonds defined for protein. 975 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: 2.27 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.31: 1222 1.31 - 1.60: 6089 1.60 - 1.90: 21 1.90 - 2.20: 1 2.20 - 2.50: 1 Bond restraints: 7334 Sorted by residual: bond pdb=" CB PRO A 830 " pdb=" CG PRO A 830 " ideal model delta sigma weight residual 1.492 2.498 -1.006 5.00e-02 4.00e+02 4.05e+02 bond pdb=" CG PRO A 830 " pdb=" CD PRO A 830 " ideal model delta sigma weight residual 1.503 1.007 0.496 3.40e-02 8.65e+02 2.13e+02 bond pdb=" CB PRO A 794 " pdb=" CG PRO A 794 " ideal model delta sigma weight residual 1.492 2.086 -0.594 5.00e-02 4.00e+02 1.41e+02 bond pdb=" CG PRO A 723 " pdb=" CD PRO A 723 " ideal model delta sigma weight residual 1.503 1.115 0.388 3.40e-02 8.65e+02 1.30e+02 bond pdb=" CB PRO A 723 " pdb=" CG PRO A 723 " ideal model delta sigma weight residual 1.492 1.020 0.472 5.00e-02 4.00e+02 8.93e+01 ... (remaining 7329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 17.39: 9961 17.39 - 34.79: 8 34.79 - 52.18: 0 52.18 - 69.57: 1 69.57 - 86.97: 2 Bond angle restraints: 9972 Sorted by residual: angle pdb=" CB PRO A 830 " pdb=" CG PRO A 830 " pdb=" CD PRO A 830 " ideal model delta sigma weight residual 106.10 19.13 86.97 3.20e+00 9.77e-02 7.39e+02 angle pdb=" CA PRO A 794 " pdb=" N PRO A 794 " pdb=" CD PRO A 794 " ideal model delta sigma weight residual 112.00 78.00 34.00 1.40e+00 5.10e-01 5.90e+02 angle pdb=" CB PRO A 723 " pdb=" CG PRO A 723 " pdb=" CD PRO A 723 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CB PRO A 794 " pdb=" CG PRO A 794 " pdb=" CD PRO A 794 " ideal model delta sigma weight residual 106.10 39.67 66.43 3.20e+00 9.77e-02 4.31e+02 angle pdb=" CA PRO A 723 " pdb=" CB PRO A 723 " pdb=" CG PRO A 723 " ideal model delta sigma weight residual 104.50 70.40 34.10 1.90e+00 2.77e-01 3.22e+02 ... (remaining 9967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 4247 26.67 - 53.33: 148 53.33 - 80.00: 27 80.00 - 106.66: 5 106.66 - 133.33: 1 Dihedral angle restraints: 4428 sinusoidal: 1816 harmonic: 2612 Sorted by residual: dihedral pdb=" N PRO A 830 " pdb=" CG PRO A 830 " pdb=" CD PRO A 830 " pdb=" CB PRO A 830 " ideal model delta sinusoidal sigma weight residual -30.00 -163.33 133.33 1 1.50e+01 4.44e-03 7.19e+01 dihedral pdb=" N PRO A 794 " pdb=" CG PRO A 794 " pdb=" CD PRO A 794 " pdb=" CB PRO A 794 " ideal model delta sinusoidal sigma weight residual -30.00 -131.21 101.21 1 1.50e+01 4.44e-03 5.10e+01 dihedral pdb=" CA ILE A 336 " pdb=" C ILE A 336 " pdb=" N THR A 337 " pdb=" CA THR A 337 " ideal model delta harmonic sigma weight residual 180.00 149.20 30.80 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 4425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 732 0.037 - 0.074: 264 0.074 - 0.111: 89 0.111 - 0.148: 29 0.148 - 0.184: 3 Chirality restraints: 1117 Sorted by residual: chirality pdb=" CB THR A 167 " pdb=" CA THR A 167 " pdb=" OG1 THR A 167 " pdb=" CG2 THR A 167 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CG LEU A1051 " pdb=" CB LEU A1051 " pdb=" CD1 LEU A1051 " pdb=" CD2 LEU A1051 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE A 681 " pdb=" N ILE A 681 " pdb=" C ILE A 681 " pdb=" CB ILE A 681 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1114 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 793 " 0.101 5.00e-02 4.00e+02 1.29e-01 2.67e+01 pdb=" N PRO A 794 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 794 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 794 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 681 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A 682 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 122 " -0.062 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO A 123 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.053 5.00e-02 4.00e+02 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 25 2.41 - 3.03: 4293 3.03 - 3.66: 10874 3.66 - 4.28: 17076 4.28 - 4.90: 28338 Nonbonded interactions: 60606 Sorted by model distance: nonbonded pdb=" O TYR A 74 " pdb=" OE1 GLU A 78 " model vdw 1.791 3.040 nonbonded pdb=" O GLN A 410 " pdb=" OE1 GLU A 414 " model vdw 2.051 3.040 nonbonded pdb=" OD1 ASN A 331 " pdb=" N THR A 332 " model vdw 2.093 3.120 nonbonded pdb=" NZ LYS A 848 " pdb=" OE2 GLU A1039 " model vdw 2.208 3.120 nonbonded pdb=" O ASP A 609 " pdb=" NZ LYS A 615 " model vdw 2.211 3.120 ... (remaining 60601 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: 4.840 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.230 Find NCS groups from input model: 0.070 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:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.018 1.006 7334 Z= 1.116 Angle : 1.706 86.966 9972 Z= 0.740 Chirality : 0.045 0.184 1117 Planarity : 0.010 0.129 1293 Dihedral : 14.575 133.327 2722 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.62 (0.28), residues: 885 helix: 1.32 (0.24), residues: 395 sheet: -0.31 (0.43), residues: 119 loop : -0.22 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 399 HIS 0.006 0.001 HIS A 577 PHE 0.018 0.002 PHE A 773 TYR 0.014 0.001 TYR A 676 ARG 0.007 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.758 Fit side-chains REVERT: A 342 ILE cc_start: 0.8255 (mm) cc_final: 0.7976 (mm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 1.4479 time to fit residues: 232.0700 Evaluate side-chains 109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 23 GLN A 25 GLN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN A 400 HIS A 692 ASN A 857 ASN ** A 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 995 GLN A 998 ASN A 999 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.165207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128358 restraints weight = 7787.408| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.19 r_work: 0.3438 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7334 Z= 0.277 Angle : 0.625 12.389 9972 Z= 0.321 Chirality : 0.044 0.147 1117 Planarity : 0.008 0.094 1293 Dihedral : 4.674 31.804 954 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.08 % Allowed : 8.23 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.79 (0.28), residues: 885 helix: 1.63 (0.25), residues: 400 sheet: -0.62 (0.44), residues: 119 loop : -0.23 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS A 400 PHE 0.015 0.002 PHE A 626 TYR 0.014 0.001 TYR A 676 ARG 0.007 0.001 ARG A1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.734 Fit side-chains REVERT: A 118 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: A 142 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6060 (tm-30) REVERT: A 242 LEU cc_start: 0.8328 (mp) cc_final: 0.7925 (tp) REVERT: A 342 ILE cc_start: 0.7889 (mm) cc_final: 0.7563 (mm) REVERT: A 586 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 649 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6092 (tm-30) REVERT: A 731 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7758 (mp0) REVERT: A 1059 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6842 (mtt90) outliers start: 24 outliers final: 7 residues processed: 123 average time/residue: 1.5040 time to fit residues: 193.3902 Evaluate side-chains 114 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 85 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 0.0770 chunk 86 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A 973 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.168155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131776 restraints weight = 7938.475| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.18 r_work: 0.3497 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7334 Z= 0.205 Angle : 0.532 6.286 9972 Z= 0.275 Chirality : 0.042 0.139 1117 Planarity : 0.007 0.058 1293 Dihedral : 4.455 30.549 954 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.47 % Allowed : 10.03 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.07 (0.29), residues: 885 helix: 1.90 (0.25), residues: 402 sheet: -0.55 (0.44), residues: 124 loop : -0.11 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.008 0.001 HIS A 999 PHE 0.013 0.002 PHE A 626 TYR 0.012 0.001 TYR A 676 ARG 0.008 0.001 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.793 Fit side-chains REVERT: A 142 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6135 (tm-30) REVERT: A 242 LEU cc_start: 0.8350 (mp) cc_final: 0.7970 (tp) REVERT: A 342 ILE cc_start: 0.7926 (mm) cc_final: 0.7693 (mm) REVERT: A 586 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: A 649 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6134 (tm-30) REVERT: A 731 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7728 (mp0) REVERT: A 975 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7439 (tt0) REVERT: A 995 GLN cc_start: 0.7499 (mp-120) cc_final: 0.7069 (mp10) REVERT: A 1059 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6903 (mtt90) outliers start: 27 outliers final: 11 residues processed: 128 average time/residue: 1.3675 time to fit residues: 183.8960 Evaluate side-chains 119 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 370 GLN A 857 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127163 restraints weight = 7910.477| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.21 r_work: 0.3425 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7334 Z= 0.268 Angle : 0.546 5.339 9972 Z= 0.282 Chirality : 0.043 0.144 1117 Planarity : 0.006 0.054 1293 Dihedral : 4.519 29.519 954 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.98 % Allowed : 11.05 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 885 helix: 1.89 (0.25), residues: 394 sheet: -0.61 (0.45), residues: 119 loop : -0.05 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 999 PHE 0.016 0.002 PHE A 626 TYR 0.015 0.001 TYR A 294 ARG 0.008 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.739 Fit side-chains REVERT: A 118 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: A 142 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6018 (tm-30) REVERT: A 242 LEU cc_start: 0.8377 (mp) cc_final: 0.7982 (tp) REVERT: A 342 ILE cc_start: 0.8068 (mm) cc_final: 0.7758 (mm) REVERT: A 393 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7438 (mp-120) REVERT: A 586 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: A 731 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7852 (mp0) REVERT: A 971 ASP cc_start: 0.7537 (m-30) cc_final: 0.7250 (m-30) REVERT: A 975 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7384 (tt0) REVERT: A 1059 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6864 (mtt90) outliers start: 31 outliers final: 14 residues processed: 127 average time/residue: 1.2591 time to fit residues: 168.4987 Evaluate side-chains 124 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.0370 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A 995 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128184 restraints weight = 7879.852| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.21 r_work: 0.3435 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7334 Z= 0.218 Angle : 0.513 5.033 9972 Z= 0.266 Chirality : 0.042 0.139 1117 Planarity : 0.006 0.053 1293 Dihedral : 4.401 28.886 954 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.98 % Allowed : 11.83 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 885 helix: 1.99 (0.26), residues: 394 sheet: -0.64 (0.45), residues: 119 loop : -0.03 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.006 0.001 HIS A 999 PHE 0.014 0.001 PHE A 626 TYR 0.014 0.001 TYR A 294 ARG 0.009 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.740 Fit side-chains REVERT: A 142 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6005 (tm-30) REVERT: A 242 LEU cc_start: 0.8367 (mp) cc_final: 0.7967 (tp) REVERT: A 256 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6644 (mt-10) REVERT: A 342 ILE cc_start: 0.8054 (mm) cc_final: 0.7747 (mm) REVERT: A 586 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: A 649 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6168 (tm-30) REVERT: A 971 ASP cc_start: 0.7526 (m-30) cc_final: 0.7236 (m-30) REVERT: A 975 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7368 (tt0) REVERT: A 1059 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6832 (mtt90) outliers start: 31 outliers final: 15 residues processed: 128 average time/residue: 1.2454 time to fit residues: 168.1495 Evaluate side-chains 124 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN A 857 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.165088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128077 restraints weight = 7862.119| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.21 r_work: 0.3431 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7334 Z= 0.219 Angle : 0.513 5.058 9972 Z= 0.267 Chirality : 0.042 0.138 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.364 27.985 954 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.86 % Allowed : 13.62 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.29), residues: 885 helix: 1.91 (0.25), residues: 402 sheet: -0.63 (0.46), residues: 117 loop : -0.07 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.006 0.001 HIS A 577 PHE 0.014 0.001 PHE A 626 TYR 0.014 0.001 TYR A 294 ARG 0.008 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.747 Fit side-chains REVERT: A 71 GLU cc_start: 0.7452 (pm20) cc_final: 0.7244 (pm20) REVERT: A 118 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: A 142 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: A 242 LEU cc_start: 0.8372 (mp) cc_final: 0.8067 (tt) REVERT: A 342 ILE cc_start: 0.8059 (mm) cc_final: 0.7758 (mm) REVERT: A 586 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: A 649 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6202 (tm-30) REVERT: A 971 ASP cc_start: 0.7445 (m-30) cc_final: 0.7166 (m-30) REVERT: A 975 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7372 (tt0) REVERT: A 995 GLN cc_start: 0.7521 (mp-120) cc_final: 0.6938 (mp10) REVERT: A 1049 ASP cc_start: 0.7590 (m-30) cc_final: 0.7297 (m-30) REVERT: A 1059 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6835 (mtt90) outliers start: 30 outliers final: 16 residues processed: 125 average time/residue: 1.4737 time to fit residues: 194.6452 Evaluate side-chains 124 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 857 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.164644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127621 restraints weight = 7834.069| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.20 r_work: 0.3424 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7334 Z= 0.238 Angle : 0.520 5.154 9972 Z= 0.270 Chirality : 0.043 0.139 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.391 27.445 954 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.21 % Allowed : 14.40 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 885 helix: 1.95 (0.25), residues: 394 sheet: -0.62 (0.45), residues: 119 loop : -0.05 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS A 577 PHE 0.015 0.001 PHE A 626 TYR 0.015 0.001 TYR A 294 ARG 0.009 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.904 Fit side-chains REVERT: A 142 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6028 (tm-30) REVERT: A 242 LEU cc_start: 0.8388 (mp) cc_final: 0.8081 (tt) REVERT: A 342 ILE cc_start: 0.8003 (mm) cc_final: 0.7670 (mm) REVERT: A 586 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: A 649 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: A 971 ASP cc_start: 0.7433 (m-30) cc_final: 0.7170 (m-30) REVERT: A 975 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7337 (tt0) REVERT: A 995 GLN cc_start: 0.7502 (mp-120) cc_final: 0.6916 (mp10) REVERT: A 1059 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6827 (mtt90) outliers start: 25 outliers final: 16 residues processed: 121 average time/residue: 1.6872 time to fit residues: 215.1755 Evaluate side-chains 122 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN A 292 ASN A 369 GLN A 857 ASN A1008 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.164982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127991 restraints weight = 7924.258| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.21 r_work: 0.3427 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7334 Z= 0.225 Angle : 0.513 5.156 9972 Z= 0.266 Chirality : 0.043 0.139 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.360 27.074 954 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.08 % Allowed : 14.65 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.29), residues: 885 helix: 1.95 (0.25), residues: 396 sheet: -0.54 (0.45), residues: 124 loop : -0.04 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.007 0.001 HIS A 577 PHE 0.014 0.001 PHE A 626 TYR 0.015 0.001 TYR A 294 ARG 0.007 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.827 Fit side-chains REVERT: A 71 GLU cc_start: 0.7404 (pm20) cc_final: 0.7195 (pm20) REVERT: A 142 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6029 (tm-30) REVERT: A 242 LEU cc_start: 0.8380 (mp) cc_final: 0.8073 (tt) REVERT: A 256 GLU cc_start: 0.6913 (mt-10) cc_final: 0.5712 (pm20) REVERT: A 342 ILE cc_start: 0.7999 (mm) cc_final: 0.7671 (mm) REVERT: A 586 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: A 611 MET cc_start: 0.7653 (mpp) cc_final: 0.7252 (tpp) REVERT: A 649 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6189 (tm-30) REVERT: A 966 GLN cc_start: 0.6992 (mm-40) cc_final: 0.6612 (tp-100) REVERT: A 971 ASP cc_start: 0.7433 (m-30) cc_final: 0.7182 (m-30) REVERT: A 975 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7414 (tp-100) REVERT: A 995 GLN cc_start: 0.7527 (mp-120) cc_final: 0.6932 (mp10) REVERT: A 1049 ASP cc_start: 0.7616 (m-30) cc_final: 0.7356 (m-30) REVERT: A 1059 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6830 (mtt90) outliers start: 24 outliers final: 13 residues processed: 126 average time/residue: 1.2936 time to fit residues: 171.7624 Evaluate side-chains 124 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN A 369 GLN A 857 ASN A1008 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.164623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127550 restraints weight = 7929.021| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.21 r_work: 0.3444 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7334 Z= 0.238 Angle : 0.524 5.218 9972 Z= 0.272 Chirality : 0.043 0.144 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.379 26.638 954 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.70 % Allowed : 15.81 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 885 helix: 1.92 (0.25), residues: 396 sheet: -0.54 (0.45), residues: 124 loop : -0.05 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.007 0.001 HIS A 577 PHE 0.015 0.001 PHE A 626 TYR 0.016 0.001 TYR A 294 ARG 0.003 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.904 Fit side-chains REVERT: A 71 GLU cc_start: 0.7467 (pm20) cc_final: 0.7258 (pm20) REVERT: A 142 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: A 242 LEU cc_start: 0.8389 (mp) cc_final: 0.8085 (tt) REVERT: A 256 GLU cc_start: 0.6889 (mt-10) cc_final: 0.5730 (pm20) REVERT: A 342 ILE cc_start: 0.8031 (mm) cc_final: 0.7700 (mm) REVERT: A 586 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: A 611 MET cc_start: 0.7667 (mpp) cc_final: 0.7267 (tpp) REVERT: A 649 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6164 (tm-30) REVERT: A 966 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6674 (tp-100) REVERT: A 971 ASP cc_start: 0.7429 (m-30) cc_final: 0.7194 (m-30) REVERT: A 975 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7346 (tt0) REVERT: A 995 GLN cc_start: 0.7472 (mp-120) cc_final: 0.6857 (mp10) REVERT: A 1049 ASP cc_start: 0.7602 (m-30) cc_final: 0.7354 (m-30) REVERT: A 1059 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6892 (mtt90) outliers start: 21 outliers final: 14 residues processed: 121 average time/residue: 1.5645 time to fit residues: 201.3567 Evaluate side-chains 124 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 2 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 57 optimal weight: 0.2980 chunk 75 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN A 369 GLN A 857 ASN A1008 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130838 restraints weight = 7981.520| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.20 r_work: 0.3481 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7334 Z= 0.199 Angle : 0.506 5.004 9972 Z= 0.263 Chirality : 0.043 0.160 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.287 26.349 954 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.57 % Allowed : 15.94 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 885 helix: 2.02 (0.25), residues: 396 sheet: -0.57 (0.45), residues: 124 loop : -0.04 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.007 0.001 HIS A 577 PHE 0.012 0.001 PHE A 112 TYR 0.014 0.001 TYR A 294 ARG 0.005 0.000 ARG A 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.747 Fit side-chains REVERT: A 71 GLU cc_start: 0.7374 (pm20) cc_final: 0.7162 (pm20) REVERT: A 142 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6101 (tm-30) REVERT: A 242 LEU cc_start: 0.8375 (mp) cc_final: 0.8090 (tt) REVERT: A 256 GLU cc_start: 0.6833 (mt-10) cc_final: 0.5905 (pm20) REVERT: A 342 ILE cc_start: 0.8009 (mm) cc_final: 0.7705 (mm) REVERT: A 586 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: A 611 MET cc_start: 0.7781 (mpp) cc_final: 0.7340 (mmm) REVERT: A 649 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6123 (tm-30) REVERT: A 966 GLN cc_start: 0.7082 (mm-40) cc_final: 0.6650 (tp-100) REVERT: A 971 ASP cc_start: 0.7417 (m-30) cc_final: 0.7179 (m-30) REVERT: A 975 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7352 (tp-100) REVERT: A 995 GLN cc_start: 0.7525 (mp-120) cc_final: 0.7037 (mp10) REVERT: A 1049 ASP cc_start: 0.7710 (m-30) cc_final: 0.7470 (m-30) REVERT: A 1059 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6958 (mtt90) outliers start: 20 outliers final: 15 residues processed: 126 average time/residue: 1.5580 time to fit residues: 206.5414 Evaluate side-chains 127 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN A 369 GLN A 857 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128967 restraints weight = 7868.104| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.17 r_work: 0.3458 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7334 Z= 0.266 Angle : 0.549 5.467 9972 Z= 0.284 Chirality : 0.044 0.261 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.429 25.934 954 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.96 % Allowed : 15.68 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 885 helix: 1.83 (0.25), residues: 396 sheet: -0.62 (0.44), residues: 124 loop : -0.06 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.007 0.001 HIS A 577 PHE 0.016 0.002 PHE A 626 TYR 0.016 0.001 TYR A 294 ARG 0.007 0.001 ARG A 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6924.15 seconds wall clock time: 122 minutes 11.50 seconds (7331.50 seconds total)