Starting phenix.real_space_refine on Sun May 11 01:22:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qy7_18747/05_2025/8qy7_18747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qy7_18747/05_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_18747/05_2025/8qy7_18747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qy7_18747/05_2025/8qy7_18747.map" model { file = "/net/cci-nas-00/data/ceres_data/8qy7_18747/05_2025/8qy7_18747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qy7_18747/05_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-5687/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: 5.30, per 1000 atoms: 0.74 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: 1.73 Conformation dependent library (CDL) restraints added in 994.8 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: 0.93 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: 2.52 Time building geometry restraints manager: 2.05 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.230 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.090 ------------------------------------------------------------------------------- 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= 0.489 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 Details of bonding type rmsd hydrogen bonds : bond 0.14021 ( 340) hydrogen bonds : angle 6.20178 ( 975) covalent geometry : bond 0.01795 ( 7334) covalent geometry : angle 1.70636 ( 9972) *********************** 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 : 0.765 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: 1.5293 time to fit residues: 244.7053 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 : 0.874 ------------------------------------------------------------------------------- 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 = 7787.406| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.19 r_work: 0.3453 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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= 0.173 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 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 340) hydrogen bonds : angle 4.91509 ( 975) covalent geometry : bond 0.00422 ( 7334) covalent geometry : angle 0.62510 ( 9972) *********************** 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 : 0.816 Fit side-chains REVERT: A 118 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 142 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6044 (tm-30) REVERT: A 242 LEU cc_start: 0.8324 (mp) cc_final: 0.7919 (tp) REVERT: A 342 ILE cc_start: 0.7881 (mm) cc_final: 0.7557 (mm) REVERT: A 586 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 649 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6079 (tm-30) REVERT: A 731 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7749 (mp0) REVERT: A 1059 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6835 (mtt90) outliers start: 24 outliers final: 7 residues processed: 123 average time/residue: 1.4054 time to fit residues: 181.1713 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 : 0.727 ------------------------------------------------------------------------------- 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: 1.9990 chunk 83 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 0.0970 chunk 86 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.165119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128053 restraints weight = 7965.377| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.22 r_work: 0.3435 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7334 Z= 0.151 Angle : 0.552 6.428 9972 Z= 0.285 Chirality : 0.043 0.142 1117 Planarity : 0.007 0.058 1293 Dihedral : 4.535 30.359 954 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.60 % Allowed : 10.03 % Favored : 86.38 % 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: 1.01 (0.28), residues: 885 helix: 1.89 (0.25), residues: 394 sheet: -0.63 (0.45), residues: 119 loop : -0.13 (0.33), residues: 372 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 0.014 0.002 PHE A 626 TYR 0.013 0.001 TYR A 294 ARG 0.008 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 340) hydrogen bonds : angle 4.62310 ( 975) covalent geometry : bond 0.00366 ( 7334) covalent geometry : angle 0.55227 ( 9972) *********************** 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 140 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.775 Fit side-chains REVERT: A 78 GLU cc_start: 0.7296 (mp0) cc_final: 0.6669 (mp0) REVERT: A 118 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: A 142 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.5963 (tm-30) REVERT: A 242 LEU cc_start: 0.8353 (mp) cc_final: 0.7936 (tp) REVERT: A 342 ILE cc_start: 0.7998 (mm) cc_final: 0.7628 (mm) REVERT: A 586 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: A 649 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6160 (tm-30) REVERT: A 731 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7744 (mp0) REVERT: A 971 ASP cc_start: 0.7551 (m-30) cc_final: 0.7279 (m-30) REVERT: A 975 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7371 (tt0) REVERT: A 1059 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6845 (mtt90) outliers start: 28 outliers final: 12 residues processed: 130 average time/residue: 1.3620 time to fit residues: 185.9557 Evaluate side-chains 123 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE 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 237 SER 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 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: 0.0020 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.0000 chunk 59 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 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 = 0.3946 r_free = 0.3946 target = 0.167638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131184 restraints weight = 7860.704| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.18 r_work: 0.3488 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7334 Z= 0.128 Angle : 0.511 4.942 9972 Z= 0.265 Chirality : 0.042 0.139 1117 Planarity : 0.006 0.054 1293 Dihedral : 4.380 29.715 954 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.60 % Allowed : 11.05 % Favored : 85.35 % 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: 1.19 (0.29), residues: 885 helix: 2.04 (0.26), residues: 396 sheet: -0.60 (0.45), residues: 119 loop : -0.03 (0.34), residues: 370 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 0.013 0.001 PHE A 626 TYR 0.013 0.001 TYR A 294 ARG 0.006 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 340) hydrogen bonds : angle 4.43981 ( 975) covalent geometry : bond 0.00308 ( 7334) covalent geometry : angle 0.51149 ( 9972) *********************** 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 138 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.743 Fit side-chains REVERT: A 65 ARG cc_start: 0.7658 (ptt-90) cc_final: 0.7409 (ptt90) REVERT: A 71 GLU cc_start: 0.7441 (pm20) cc_final: 0.7231 (pm20) REVERT: A 142 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6090 (tm-30) REVERT: A 242 LEU cc_start: 0.8363 (mp) cc_final: 0.8001 (tp) REVERT: A 342 ILE cc_start: 0.8019 (mm) cc_final: 0.7724 (mm) REVERT: A 586 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: A 649 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6159 (tm-30) REVERT: A 971 ASP cc_start: 0.7530 (m-30) cc_final: 0.7247 (m-30) REVERT: A 975 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7425 (tt0) REVERT: A 1049 ASP cc_start: 0.7634 (m-30) cc_final: 0.7374 (m-30) REVERT: A 1059 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6860 (mtt90) outliers start: 28 outliers final: 12 residues processed: 128 average time/residue: 1.2371 time to fit residues: 166.7949 Evaluate side-chains 120 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LYS 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 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: 0.8980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.165071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128106 restraints weight = 7873.786| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.21 r_work: 0.3421 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1971 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= 0.147 Angle : 0.522 5.103 9972 Z= 0.270 Chirality : 0.043 0.141 1117 Planarity : 0.006 0.053 1293 Dihedral : 4.385 28.656 954 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.98 % Allowed : 12.34 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.26), residues: 394 sheet: -0.66 (0.46), residues: 117 loop : -0.07 (0.34), residues: 374 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 0.015 0.002 PHE A 626 TYR 0.015 0.001 TYR A 294 ARG 0.008 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 340) hydrogen bonds : angle 4.42968 ( 975) covalent geometry : bond 0.00354 ( 7334) covalent geometry : angle 0.52185 ( 9972) *********************** 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 : 1.204 Fit side-chains REVERT: A 118 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: A 142 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6006 (tm-30) REVERT: A 242 LEU cc_start: 0.8360 (mp) cc_final: 0.7962 (tp) REVERT: A 342 ILE cc_start: 0.8037 (mm) cc_final: 0.7733 (mm) REVERT: A 393 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7574 (mp-120) REVERT: A 586 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: A 971 ASP cc_start: 0.7433 (m-30) cc_final: 0.7117 (m-30) REVERT: A 975 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7322 (tt0) REVERT: A 995 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6940 (mp10) REVERT: A 1049 ASP cc_start: 0.7576 (m-30) cc_final: 0.7295 (m-30) REVERT: A 1059 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6823 (mtt90) outliers start: 31 outliers final: 17 residues processed: 128 average time/residue: 1.2735 time to fit residues: 172.3273 Evaluate side-chains 129 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN 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: 0.8980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.0050 chunk 49 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.167279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130699 restraints weight = 7821.253| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.18 r_work: 0.3482 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1994 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= 0.130 Angle : 0.505 5.052 9972 Z= 0.262 Chirality : 0.042 0.137 1117 Planarity : 0.005 0.053 1293 Dihedral : 4.328 28.231 954 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.98 % Allowed : 13.24 % Favored : 82.78 % 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: 1.18 (0.29), residues: 885 helix: 2.04 (0.26), residues: 396 sheet: -0.66 (0.45), residues: 119 loop : -0.02 (0.34), residues: 370 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 0.013 0.001 PHE A 626 TYR 0.014 0.001 TYR A 294 ARG 0.008 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 340) hydrogen bonds : angle 4.35850 ( 975) covalent geometry : bond 0.00310 ( 7334) covalent geometry : angle 0.50478 ( 9972) *********************** 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 139 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.904 Fit side-chains REVERT: A 71 GLU cc_start: 0.7437 (pm20) cc_final: 0.7225 (pm20) REVERT: A 142 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6107 (tm-30) REVERT: A 242 LEU cc_start: 0.8378 (mp) cc_final: 0.8086 (tp) REVERT: A 342 ILE cc_start: 0.8083 (mm) cc_final: 0.7798 (mm) REVERT: A 393 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7616 (mp-120) REVERT: A 586 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: A 649 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6181 (tm-30) REVERT: A 971 ASP cc_start: 0.7438 (m-30) cc_final: 0.7169 (m-30) REVERT: A 975 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7376 (tt0) REVERT: A 995 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6882 (mp10) REVERT: A 1049 ASP cc_start: 0.7681 (m-30) cc_final: 0.7443 (m-30) REVERT: A 1059 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6876 (mtt90) outliers start: 31 outliers final: 17 residues processed: 127 average time/residue: 1.2478 time to fit residues: 167.6664 Evaluate side-chains 128 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 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 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 995 GLN 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: 3.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 82 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 A 995 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131071 restraints weight = 7782.454| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.17 r_work: 0.3486 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2071 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= 0.127 Angle : 0.501 5.036 9972 Z= 0.260 Chirality : 0.042 0.136 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.294 27.813 954 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.98 % Allowed : 12.98 % Favored : 83.03 % 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: 1.19 (0.29), residues: 885 helix: 2.06 (0.25), residues: 396 sheet: -0.66 (0.45), residues: 119 loop : -0.03 (0.34), residues: 370 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 0.013 0.001 PHE A 626 TYR 0.014 0.001 TYR A 294 ARG 0.009 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 340) hydrogen bonds : angle 4.32600 ( 975) covalent geometry : bond 0.00302 ( 7334) covalent geometry : angle 0.50136 ( 9972) *********************** 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 142 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.786 Fit side-chains REVERT: A 71 GLU cc_start: 0.7432 (pm20) cc_final: 0.7222 (pm20) REVERT: A 142 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6109 (tm-30) REVERT: A 242 LEU cc_start: 0.8376 (mp) cc_final: 0.8094 (tt) REVERT: A 256 GLU cc_start: 0.6918 (mt-10) cc_final: 0.5922 (pm20) REVERT: A 342 ILE cc_start: 0.8074 (mm) cc_final: 0.7767 (mm) REVERT: A 393 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7600 (mp-120) REVERT: A 586 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: A 649 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: A 971 ASP cc_start: 0.7426 (m-30) cc_final: 0.7168 (m-30) REVERT: A 975 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7364 (tt0) REVERT: A 995 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6896 (mp10) REVERT: A 1049 ASP cc_start: 0.7680 (m-30) cc_final: 0.7432 (m-30) REVERT: A 1059 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6871 (mtt90) outliers start: 31 outliers final: 17 residues processed: 131 average time/residue: 1.2326 time to fit residues: 170.8117 Evaluate side-chains 129 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 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 995 GLN 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: 0.5980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 A 973 GLN A 995 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130641 restraints weight = 7879.526| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.19 r_work: 0.3479 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2075 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= 0.135 Angle : 0.509 5.076 9972 Z= 0.264 Chirality : 0.043 0.155 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.306 27.414 954 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.60 % Allowed : 13.88 % 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: 1.19 (0.29), residues: 885 helix: 2.04 (0.25), residues: 396 sheet: -0.60 (0.44), residues: 124 loop : -0.00 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 577 PHE 0.013 0.001 PHE A 626 TYR 0.015 0.001 TYR A 294 ARG 0.009 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 340) hydrogen bonds : angle 4.33613 ( 975) covalent geometry : bond 0.00323 ( 7334) covalent geometry : angle 0.50898 ( 9972) *********************** 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: 28 poor density : 107 time to evaluate : 0.817 Fit side-chains REVERT: A 71 GLU cc_start: 0.7434 (pm20) cc_final: 0.7222 (pm20) REVERT: A 142 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6088 (tm-30) REVERT: A 242 LEU cc_start: 0.8383 (mp) cc_final: 0.8096 (tt) REVERT: A 256 GLU cc_start: 0.6948 (mt-10) cc_final: 0.5811 (pm20) REVERT: A 342 ILE cc_start: 0.8015 (mm) cc_final: 0.7703 (mm) REVERT: A 393 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7597 (mp-120) REVERT: A 586 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: A 649 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6178 (tm-30) REVERT: A 966 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6665 (tp-100) REVERT: A 971 ASP cc_start: 0.7377 (m-30) cc_final: 0.7131 (m-30) REVERT: A 975 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7478 (tp-100) REVERT: A 995 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6874 (mp10) REVERT: A 1049 ASP cc_start: 0.7679 (m-30) cc_final: 0.7394 (m-30) REVERT: A 1059 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6846 (mtt90) outliers start: 28 outliers final: 17 residues processed: 127 average time/residue: 1.1448 time to fit residues: 153.7607 Evaluate side-chains 129 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 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 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 995 GLN 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: 2.9990 chunk 17 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 A 995 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.167272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130422 restraints weight = 7869.793| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.19 r_work: 0.3478 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7334 Z= 0.137 Angle : 0.515 5.061 9972 Z= 0.267 Chirality : 0.043 0.239 1117 Planarity : 0.005 0.055 1293 Dihedral : 4.313 27.115 954 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.47 % Allowed : 14.27 % 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: 1.18 (0.29), residues: 885 helix: 2.02 (0.25), residues: 396 sheet: -0.60 (0.44), residues: 124 loop : -0.00 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 577 PHE 0.013 0.001 PHE A 626 TYR 0.015 0.001 TYR A 294 ARG 0.011 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 340) hydrogen bonds : angle 4.36550 ( 975) covalent geometry : bond 0.00328 ( 7334) covalent geometry : angle 0.51453 ( 9972) *********************** 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 136 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.759 Fit side-chains REVERT: A 71 GLU cc_start: 0.7419 (pm20) cc_final: 0.7207 (pm20) REVERT: A 142 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6094 (tm-30) REVERT: A 242 LEU cc_start: 0.8385 (mp) cc_final: 0.8097 (tt) REVERT: A 256 GLU cc_start: 0.6884 (mt-10) cc_final: 0.5840 (pm20) REVERT: A 342 ILE cc_start: 0.8014 (mm) cc_final: 0.7701 (mm) REVERT: A 393 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7543 (mp-120) REVERT: A 586 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: A 649 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6168 (tm-30) REVERT: A 966 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6669 (tp-100) REVERT: A 971 ASP cc_start: 0.7379 (m-30) cc_final: 0.7129 (m-30) REVERT: A 975 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7360 (tt0) REVERT: A 995 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6813 (mp10) REVERT: A 1049 ASP cc_start: 0.7670 (m-30) cc_final: 0.7410 (m-30) REVERT: A 1059 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6886 (mtt90) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 1.2513 time to fit residues: 169.1135 Evaluate side-chains 128 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 247 SER 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 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 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 995 GLN 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: 0.6980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 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 22 ASN A 243 GLN A 369 GLN A 857 ASN A 995 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127772 restraints weight = 8043.986| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.23 r_work: 0.3426 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2132 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= 0.152 Angle : 0.533 7.176 9972 Z= 0.274 Chirality : 0.044 0.274 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.359 26.640 954 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.96 % Allowed : 15.17 % Favored : 81.88 % 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: 1.11 (0.29), residues: 885 helix: 1.94 (0.25), residues: 396 sheet: -0.61 (0.44), residues: 124 loop : -0.02 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 577 PHE 0.015 0.001 PHE A 626 TYR 0.016 0.001 TYR A 294 ARG 0.005 0.000 ARG A 820 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 340) hydrogen bonds : angle 4.42796 ( 975) covalent geometry : bond 0.00366 ( 7334) covalent geometry : angle 0.53257 ( 9972) ********************** 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 129 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.739 Fit side-chains REVERT: A 71 GLU cc_start: 0.7449 (pm20) cc_final: 0.7236 (pm20) REVERT: A 142 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: A 242 LEU cc_start: 0.8389 (mp) cc_final: 0.8079 (tt) REVERT: A 256 GLU cc_start: 0.6873 (mt-10) cc_final: 0.5803 (pm20) REVERT: A 342 ILE cc_start: 0.8009 (mm) cc_final: 0.7671 (mm) REVERT: A 393 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7456 (mp-120) REVERT: A 586 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: A 649 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6155 (tm-30) REVERT: A 966 GLN cc_start: 0.7037 (mm-40) cc_final: 0.6639 (tp-100) REVERT: A 971 ASP cc_start: 0.7390 (m-30) cc_final: 0.7133 (m-30) REVERT: A 975 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7332 (tt0) REVERT: A 995 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6724 (mp10) REVERT: A 1049 ASP cc_start: 0.7641 (m-30) cc_final: 0.7371 (m-30) REVERT: A 1059 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6882 (mtt90) outliers start: 23 outliers final: 17 residues processed: 121 average time/residue: 1.2482 time to fit residues: 159.1426 Evaluate side-chains 130 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 247 SER 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 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 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 995 GLN 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: 0.5980 chunk 79 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 A 995 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.167094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130112 restraints weight = 7827.559| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.20 r_work: 0.3457 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2173 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= 0.136 Angle : 0.523 6.902 9972 Z= 0.270 Chirality : 0.043 0.262 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.328 26.519 954 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.21 % Allowed : 15.04 % Favored : 81.75 % 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: 1.14 (0.29), residues: 885 helix: 1.97 (0.25), residues: 396 sheet: -0.61 (0.44), residues: 124 loop : -0.01 (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 0.005 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 340) hydrogen bonds : angle 4.39972 ( 975) covalent geometry : bond 0.00325 ( 7334) covalent geometry : angle 0.52346 ( 9972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6413.95 seconds wall clock time: 111 minutes 5.46 seconds (6665.46 seconds total)