Starting phenix.real_space_refine on Tue Feb 3 17:58:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jme_61599/02_2026/9jme_61599.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jme_61599/02_2026/9jme_61599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jme_61599/02_2026/9jme_61599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jme_61599/02_2026/9jme_61599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jme_61599/02_2026/9jme_61599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jme_61599/02_2026/9jme_61599.map" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 23 5.16 5 C 3643 2.51 5 N 988 2.21 5 O 1095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5749 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3960 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 471} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 0.97, per 1000 atoms: 0.17 Number of scatterers: 5749 At special positions: 0 Unit cell: (122.85, 79.3, 159.25, 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 23 16.00 O 1095 8.00 N 988 7.00 C 3643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 399 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 300.8 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 14 sheets defined 20.4% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.863A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.696A pdb=" N LYS H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.569A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.811A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.904A pdb=" N ALA A 296 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.857A pdb=" N VAL A 350 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 416 removed outlier: 4.163A pdb=" N ARG A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 522 removed outlier: 3.832A pdb=" N HIS A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 533 through 543 removed outlier: 3.836A pdb=" N GLY A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 698 through 704 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.490A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.385A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.131A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.131A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA8, first strand: chain 'A' and resid 353 through 359 removed outlier: 6.620A pdb=" N ILE A 136 " --> pdb=" O TRP A 356 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 358 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA A 134 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 353 through 359 removed outlier: 6.620A pdb=" N ILE A 136 " --> pdb=" O TRP A 356 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 358 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA A 134 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 167 through 178 removed outlier: 6.304A pdb=" N GLN A 159 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE A 172 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 157 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 174 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 155 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG A 176 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS A 153 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N TYR A 151 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 222 through 223 removed outlier: 7.099A pdb=" N LYS A 147 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP A 342 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA A 327 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 311 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AB4, first strand: chain 'A' and resid 197 through 201 Processing sheet with id=AB5, first strand: chain 'A' and resid 362 through 366 257 hydrogen bonds defined for protein. 678 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: 0.76 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1033 1.32 - 1.44: 1655 1.44 - 1.57: 3171 1.57 - 1.69: 1 1.69 - 1.81: 36 Bond restraints: 5896 Sorted by residual: bond pdb=" N PRO A 105 " pdb=" CD PRO A 105 " ideal model delta sigma weight residual 1.473 1.330 0.143 1.40e-02 5.10e+03 1.04e+02 bond pdb=" N PRO A 104 " pdb=" CD PRO A 104 " ideal model delta sigma weight residual 1.473 1.336 0.137 1.40e-02 5.10e+03 9.51e+01 bond pdb=" N PRO A 106 " pdb=" CD PRO A 106 " ideal model delta sigma weight residual 1.473 1.566 -0.093 1.40e-02 5.10e+03 4.43e+01 bond pdb=" N VAL A 112 " pdb=" CA VAL A 112 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.14e-02 7.69e+03 1.35e+01 bond pdb=" N VAL A 111 " pdb=" CA VAL A 111 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.14e-02 7.69e+03 9.14e+00 ... (remaining 5891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 7862 2.96 - 5.92: 133 5.92 - 8.88: 14 8.88 - 11.84: 2 11.84 - 14.80: 1 Bond angle restraints: 8012 Sorted by residual: angle pdb=" CA PRO A 105 " pdb=" N PRO A 105 " pdb=" CD PRO A 105 " ideal model delta sigma weight residual 112.00 122.34 -10.34 1.40e+00 5.10e-01 5.45e+01 angle pdb=" N PRO A 105 " pdb=" CA PRO A 105 " pdb=" CB PRO A 105 " ideal model delta sigma weight residual 103.08 96.02 7.06 9.70e-01 1.06e+00 5.29e+01 angle pdb=" N PRO A 105 " pdb=" CA PRO A 105 " pdb=" C PRO A 105 " ideal model delta sigma weight residual 110.70 118.42 -7.72 1.22e+00 6.72e-01 4.00e+01 angle pdb=" N ASN A 520 " pdb=" CA ASN A 520 " pdb=" C ASN A 520 " ideal model delta sigma weight residual 113.28 105.92 7.36 1.22e+00 6.72e-01 3.64e+01 angle pdb=" CA PRO A 104 " pdb=" N PRO A 104 " pdb=" CD PRO A 104 " ideal model delta sigma weight residual 112.00 119.30 -7.30 1.40e+00 5.10e-01 2.72e+01 ... (remaining 8007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 3269 15.36 - 30.71: 169 30.71 - 46.07: 50 46.07 - 61.43: 4 61.43 - 76.78: 3 Dihedral angle restraints: 3495 sinusoidal: 1375 harmonic: 2120 Sorted by residual: dihedral pdb=" CD ARG A 118 " pdb=" NE ARG A 118 " pdb=" CZ ARG A 118 " pdb=" NH1 ARG A 118 " ideal model delta sinusoidal sigma weight residual 0.00 -62.86 62.86 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA ARG A 245 " pdb=" C ARG A 245 " pdb=" N ILE A 246 " pdb=" CA ILE A 246 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ILE A 246 " pdb=" C ILE A 246 " pdb=" N GLU A 247 " pdb=" CA GLU A 247 " ideal model delta harmonic sigma weight residual 180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 3492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 574 0.050 - 0.099: 208 0.099 - 0.148: 61 0.148 - 0.198: 16 0.198 - 0.247: 6 Chirality restraints: 865 Sorted by residual: chirality pdb=" CB VAL A 488 " pdb=" CA VAL A 488 " pdb=" CG1 VAL A 488 " pdb=" CG2 VAL A 488 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL A 193 " pdb=" CA VAL A 193 " pdb=" CG1 VAL A 193 " pdb=" CG2 VAL A 193 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO A 117 " pdb=" N PRO A 117 " pdb=" C PRO A 117 " pdb=" CB PRO A 117 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 862 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 118 " 0.978 9.50e-02 1.11e+02 4.38e-01 1.16e+02 pdb=" NE ARG A 118 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 118 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 118 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 118 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 414 " 0.548 9.50e-02 1.11e+02 2.45e-01 3.68e+01 pdb=" NE ARG A 414 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 414 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 414 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 414 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 104 " -0.047 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO A 105 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " -0.048 5.00e-02 4.00e+02 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1570 2.81 - 3.33: 4616 3.33 - 3.85: 9295 3.85 - 4.38: 10776 4.38 - 4.90: 18249 Nonbonded interactions: 44506 Sorted by model distance: nonbonded pdb=" OG SER H 17 " pdb=" OE2 GLU H 82 " model vdw 2.287 3.040 nonbonded pdb=" OG SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.344 3.040 nonbonded pdb=" OH TYR A 269 " pdb=" OD2 ASP A 395 " model vdw 2.346 3.040 nonbonded pdb=" O GLY H 8 " pdb=" OG1 THR H 116 " model vdw 2.351 3.040 nonbonded pdb=" NE2 HIS A 235 " pdb=" OD1 ASP A 238 " model vdw 2.383 3.120 ... (remaining 44501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 9.050 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.700 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.007 0.143 5900 Z= 0.383 Angle : 0.975 14.796 8020 Z= 0.583 Chirality : 0.060 0.247 865 Planarity : 0.017 0.438 1033 Dihedral : 10.496 76.783 2125 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.67 % Favored : 97.05 % Rotamer: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.26), residues: 712 helix: -4.36 (0.22), residues: 105 sheet: -0.77 (0.31), residues: 248 loop : -1.87 (0.25), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 702 TYR 0.029 0.003 TYR L 92 PHE 0.041 0.004 PHE L 97 TRP 0.034 0.003 TRP H 112 HIS 0.027 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00721 ( 5896) covalent geometry : angle 0.97449 ( 8012) SS BOND : bond 0.00502 ( 4) SS BOND : angle 1.29880 ( 8) hydrogen bonds : bond 0.23765 ( 221) hydrogen bonds : angle 9.16729 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.163 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.4930 time to fit residues: 90.3635 Evaluate side-chains 102 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 235 HIS A 417 ASN A 535 ASN A 645 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108352 restraints weight = 6036.673| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.61 r_work: 0.3178 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5900 Z= 0.179 Angle : 0.622 5.494 8020 Z= 0.343 Chirality : 0.046 0.137 865 Planarity : 0.006 0.062 1033 Dihedral : 5.498 24.126 809 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.41 % Allowed : 9.11 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.27), residues: 712 helix: -0.94 (0.44), residues: 106 sheet: -0.25 (0.32), residues: 236 loop : -1.13 (0.27), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 202 TYR 0.013 0.002 TYR L 33 PHE 0.024 0.003 PHE A 146 TRP 0.017 0.002 TRP A 343 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5896) covalent geometry : angle 0.62182 ( 8012) SS BOND : bond 0.00698 ( 4) SS BOND : angle 1.07143 ( 8) hydrogen bonds : bond 0.04815 ( 221) hydrogen bonds : angle 5.76745 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.145 Fit side-chains REVERT: H 10 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7266 (tp30) REVERT: L 24 ARG cc_start: 0.7553 (tmm-80) cc_final: 0.7240 (mtp85) REVERT: A 264 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: A 314 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7805 (tp30) REVERT: A 386 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8274 (mmt90) REVERT: A 533 ASN cc_start: 0.8525 (t0) cc_final: 0.8136 (t0) REVERT: A 683 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7597 (t0) outliers start: 21 outliers final: 8 residues processed: 103 average time/residue: 0.4313 time to fit residues: 46.4732 Evaluate side-chains 93 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 683 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 22 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105443 restraints weight = 5990.716| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.61 r_work: 0.3137 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5900 Z= 0.191 Angle : 0.615 6.162 8020 Z= 0.338 Chirality : 0.046 0.142 865 Planarity : 0.005 0.069 1033 Dihedral : 5.413 22.901 809 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.41 % Allowed : 9.76 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.29), residues: 712 helix: 0.55 (0.50), residues: 106 sheet: 0.13 (0.33), residues: 235 loop : -0.78 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 202 TYR 0.012 0.002 TYR A 283 PHE 0.022 0.002 PHE A 146 TRP 0.014 0.002 TRP L 90 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 5896) covalent geometry : angle 0.61426 ( 8012) SS BOND : bond 0.00694 ( 4) SS BOND : angle 1.01239 ( 8) hydrogen bonds : bond 0.04609 ( 221) hydrogen bonds : angle 5.52713 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7225 (tp30) REVERT: L 24 ARG cc_start: 0.7612 (tmm-80) cc_final: 0.7275 (mtp85) REVERT: A 118 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7870 (mtt180) REVERT: A 264 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: A 314 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7793 (tp30) REVERT: A 386 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8212 (mtt180) REVERT: A 402 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7619 (ttm170) REVERT: A 533 ASN cc_start: 0.8597 (t0) cc_final: 0.8335 (t0) REVERT: A 683 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7644 (t0) outliers start: 21 outliers final: 11 residues processed: 90 average time/residue: 0.5255 time to fit residues: 49.3139 Evaluate side-chains 92 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 683 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 63 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104176 restraints weight = 5921.605| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.61 r_work: 0.3113 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 5900 Z= 0.224 Angle : 0.648 6.991 8020 Z= 0.355 Chirality : 0.048 0.159 865 Planarity : 0.005 0.072 1033 Dihedral : 5.506 21.320 809 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.90 % Allowed : 10.24 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.30), residues: 712 helix: 1.04 (0.51), residues: 105 sheet: 0.24 (0.33), residues: 236 loop : -0.53 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 202 TYR 0.013 0.002 TYR A 428 PHE 0.024 0.003 PHE H 99 TRP 0.016 0.002 TRP L 90 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 5896) covalent geometry : angle 0.64785 ( 8012) SS BOND : bond 0.00807 ( 4) SS BOND : angle 1.12032 ( 8) hydrogen bonds : bond 0.04678 ( 221) hydrogen bonds : angle 5.60180 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.146 Fit side-chains REVERT: H 10 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7179 (tp30) REVERT: L 24 ARG cc_start: 0.7639 (tmm-80) cc_final: 0.7267 (mtp85) REVERT: L 58 PRO cc_start: 0.8648 (Cg_exo) cc_final: 0.8369 (Cg_endo) REVERT: A 118 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7607 (mtt180) REVERT: A 264 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: A 314 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: A 386 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8199 (mtt180) REVERT: A 402 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7638 (ttm170) REVERT: A 533 ASN cc_start: 0.8620 (t0) cc_final: 0.8320 (t0) outliers start: 24 outliers final: 16 residues processed: 91 average time/residue: 0.4792 time to fit residues: 45.4961 Evaluate side-chains 98 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 683 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 417 ASN A 535 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105505 restraints weight = 6106.911| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.62 r_work: 0.3131 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5900 Z= 0.153 Angle : 0.571 6.726 8020 Z= 0.313 Chirality : 0.044 0.137 865 Planarity : 0.004 0.051 1033 Dihedral : 5.180 22.056 809 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.74 % Allowed : 10.24 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.30), residues: 712 helix: 1.43 (0.51), residues: 105 sheet: 0.34 (0.33), residues: 237 loop : -0.40 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.012 0.002 TYR A 428 PHE 0.020 0.002 PHE H 99 TRP 0.015 0.002 TRP L 90 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5896) covalent geometry : angle 0.57092 ( 8012) SS BOND : bond 0.00599 ( 4) SS BOND : angle 0.94269 ( 8) hydrogen bonds : bond 0.04090 ( 221) hydrogen bonds : angle 5.40710 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.182 Fit side-chains REVERT: H 10 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7176 (tp30) REVERT: H 82 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7006 (tp30) REVERT: L 24 ARG cc_start: 0.7620 (tmm-80) cc_final: 0.7241 (mtp85) REVERT: L 58 PRO cc_start: 0.8650 (Cg_exo) cc_final: 0.8376 (Cg_endo) REVERT: A 118 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7807 (mtt180) REVERT: A 264 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: A 533 ASN cc_start: 0.8614 (t0) cc_final: 0.8300 (t0) REVERT: A 683 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7604 (t0) outliers start: 23 outliers final: 11 residues processed: 93 average time/residue: 0.4672 time to fit residues: 45.3113 Evaluate side-chains 93 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 683 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106763 restraints weight = 5931.196| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.63 r_work: 0.3139 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5900 Z= 0.113 Angle : 0.521 6.471 8020 Z= 0.285 Chirality : 0.042 0.132 865 Planarity : 0.004 0.039 1033 Dihedral : 4.885 23.831 809 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.25 % Allowed : 10.57 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.31), residues: 712 helix: 1.71 (0.52), residues: 106 sheet: 0.54 (0.33), residues: 235 loop : -0.27 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 202 TYR 0.011 0.001 TYR A 428 PHE 0.017 0.002 PHE H 99 TRP 0.014 0.001 TRP L 90 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5896) covalent geometry : angle 0.52041 ( 8012) SS BOND : bond 0.00467 ( 4) SS BOND : angle 0.77712 ( 8) hydrogen bonds : bond 0.03610 ( 221) hydrogen bonds : angle 5.22168 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.151 Fit side-chains REVERT: H 10 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7207 (tt0) REVERT: H 73 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7814 (t70) REVERT: H 82 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6958 (tp30) REVERT: L 24 ARG cc_start: 0.7580 (tmm-80) cc_final: 0.7199 (mtp85) REVERT: L 44 LYS cc_start: 0.8778 (mttt) cc_final: 0.7964 (mmtm) REVERT: L 58 PRO cc_start: 0.8665 (Cg_exo) cc_final: 0.8419 (Cg_endo) REVERT: A 264 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: A 314 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8108 (tp30) REVERT: A 533 ASN cc_start: 0.8618 (t0) cc_final: 0.8312 (t0) REVERT: A 683 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7600 (t0) outliers start: 20 outliers final: 9 residues processed: 98 average time/residue: 0.4167 time to fit residues: 42.6842 Evaluate side-chains 96 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 683 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 8.9990 chunk 70 optimal weight: 0.0770 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106214 restraints weight = 6028.566| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.62 r_work: 0.3133 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5900 Z= 0.119 Angle : 0.523 6.702 8020 Z= 0.287 Chirality : 0.042 0.133 865 Planarity : 0.004 0.039 1033 Dihedral : 4.835 22.266 809 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.76 % Allowed : 10.73 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.31), residues: 712 helix: 2.24 (0.52), residues: 100 sheet: 0.62 (0.32), residues: 245 loop : -0.31 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 202 TYR 0.010 0.001 TYR A 428 PHE 0.017 0.002 PHE H 99 TRP 0.014 0.001 TRP L 90 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5896) covalent geometry : angle 0.52287 ( 8012) SS BOND : bond 0.00466 ( 4) SS BOND : angle 0.64885 ( 8) hydrogen bonds : bond 0.03651 ( 221) hydrogen bonds : angle 5.23386 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.138 Fit side-chains REVERT: H 10 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7195 (tt0) REVERT: H 73 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7823 (t70) REVERT: H 82 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: L 24 ARG cc_start: 0.7592 (tmm-80) cc_final: 0.7206 (mtp85) REVERT: L 44 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7943 (mmtm) REVERT: L 58 PRO cc_start: 0.8669 (Cg_exo) cc_final: 0.8420 (Cg_endo) REVERT: A 118 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7826 (mtt180) REVERT: A 264 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: A 314 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: A 533 ASN cc_start: 0.8609 (t0) cc_final: 0.8326 (t0) REVERT: A 683 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7610 (t0) outliers start: 17 outliers final: 10 residues processed: 92 average time/residue: 0.5261 time to fit residues: 50.5017 Evaluate side-chains 97 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 683 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 53 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.6364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105147 restraints weight = 5929.669| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.61 r_work: 0.3132 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5900 Z= 0.147 Angle : 0.562 6.882 8020 Z= 0.306 Chirality : 0.044 0.189 865 Planarity : 0.004 0.044 1033 Dihedral : 5.061 23.151 809 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.93 % Allowed : 10.89 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.31), residues: 712 helix: 2.13 (0.52), residues: 100 sheet: 0.55 (0.32), residues: 247 loop : -0.29 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.011 0.002 TYR H 95 PHE 0.019 0.002 PHE H 99 TRP 0.015 0.002 TRP L 90 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5896) covalent geometry : angle 0.56213 ( 8012) SS BOND : bond 0.00551 ( 4) SS BOND : angle 0.72449 ( 8) hydrogen bonds : bond 0.03932 ( 221) hydrogen bonds : angle 5.37821 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.201 Fit side-chains REVERT: H 10 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7149 (tp30) REVERT: H 73 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7844 (t70) REVERT: H 82 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6875 (tp30) REVERT: L 24 ARG cc_start: 0.7593 (tmm-80) cc_final: 0.7214 (mtp85) REVERT: L 44 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.7966 (mmtm) REVERT: L 58 PRO cc_start: 0.8662 (Cg_exo) cc_final: 0.8409 (Cg_endo) REVERT: A 118 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7829 (mtt180) REVERT: A 264 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: A 314 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8086 (tp30) REVERT: A 533 ASN cc_start: 0.8622 (t0) cc_final: 0.8336 (t0) REVERT: A 555 MET cc_start: 0.6521 (mpt) cc_final: 0.6138 (mpt) REVERT: A 683 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7668 (t0) outliers start: 18 outliers final: 10 residues processed: 89 average time/residue: 0.4662 time to fit residues: 43.2656 Evaluate side-chains 95 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 683 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.106647 restraints weight = 6027.962| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.64 r_work: 0.3129 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5900 Z= 0.123 Angle : 0.534 7.246 8020 Z= 0.290 Chirality : 0.042 0.149 865 Planarity : 0.004 0.040 1033 Dihedral : 4.904 23.802 809 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.76 % Allowed : 11.22 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.31), residues: 712 helix: 2.31 (0.52), residues: 100 sheet: 0.66 (0.32), residues: 245 loop : -0.24 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 202 TYR 0.010 0.002 TYR H 95 PHE 0.017 0.002 PHE H 99 TRP 0.014 0.001 TRP L 90 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5896) covalent geometry : angle 0.53388 ( 8012) SS BOND : bond 0.00467 ( 4) SS BOND : angle 0.70295 ( 8) hydrogen bonds : bond 0.03673 ( 221) hydrogen bonds : angle 5.22686 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.143 Fit side-chains REVERT: H 10 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7173 (tt0) REVERT: H 73 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7820 (t70) REVERT: H 82 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6839 (tp30) REVERT: L 24 ARG cc_start: 0.7590 (tmm-80) cc_final: 0.7199 (mtp85) REVERT: L 44 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.7962 (mmtm) REVERT: L 58 PRO cc_start: 0.8648 (Cg_exo) cc_final: 0.8410 (Cg_endo) REVERT: A 118 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7820 (mtt180) REVERT: A 264 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: A 314 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: A 533 ASN cc_start: 0.8601 (t0) cc_final: 0.8306 (t0) REVERT: A 555 MET cc_start: 0.6954 (mpt) cc_final: 0.6553 (mpt) REVERT: A 683 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7605 (t0) outliers start: 17 outliers final: 10 residues processed: 89 average time/residue: 0.5001 time to fit residues: 46.6372 Evaluate side-chains 97 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 683 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.0020 chunk 51 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 535 ASN A 645 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.145593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108485 restraints weight = 6052.643| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.64 r_work: 0.3185 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5900 Z= 0.093 Angle : 0.489 7.092 8020 Z= 0.265 Chirality : 0.041 0.129 865 Planarity : 0.003 0.038 1033 Dihedral : 4.588 23.804 809 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.28 % Allowed : 12.03 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.31), residues: 712 helix: 2.61 (0.53), residues: 100 sheet: 0.77 (0.32), residues: 246 loop : -0.17 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.009 0.001 TYR A 428 PHE 0.016 0.001 PHE A 274 TRP 0.012 0.001 TRP L 90 HIS 0.002 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 5896) covalent geometry : angle 0.48890 ( 8012) SS BOND : bond 0.00375 ( 4) SS BOND : angle 0.60916 ( 8) hydrogen bonds : bond 0.03223 ( 221) hydrogen bonds : angle 4.94722 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.163 Fit side-chains REVERT: H 10 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7197 (tt0) REVERT: H 73 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7803 (t70) REVERT: H 82 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: L 24 ARG cc_start: 0.7576 (tmm-80) cc_final: 0.7182 (mtp85) REVERT: L 44 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.7922 (mmtm) REVERT: A 118 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7787 (mtt180) REVERT: A 264 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: A 533 ASN cc_start: 0.8606 (t0) cc_final: 0.8309 (t0) REVERT: A 683 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7623 (t0) outliers start: 14 outliers final: 6 residues processed: 87 average time/residue: 0.5238 time to fit residues: 47.4725 Evaluate side-chains 91 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 683 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.103249 restraints weight = 5843.498| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.61 r_work: 0.3090 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 5900 Z= 0.265 Angle : 0.677 7.316 8020 Z= 0.370 Chirality : 0.050 0.215 865 Planarity : 0.006 0.081 1033 Dihedral : 5.481 21.488 809 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.93 % Allowed : 11.06 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.30), residues: 712 helix: 1.97 (0.52), residues: 99 sheet: 0.57 (0.33), residues: 241 loop : -0.24 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 386 TYR 0.015 0.003 TYR H 111 PHE 0.025 0.003 PHE H 99 TRP 0.016 0.003 TRP L 90 HIS 0.005 0.002 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00613 ( 5896) covalent geometry : angle 0.67640 ( 8012) SS BOND : bond 0.00887 ( 4) SS BOND : angle 1.02670 ( 8) hydrogen bonds : bond 0.04713 ( 221) hydrogen bonds : angle 5.59472 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.03 seconds wall clock time: 55 minutes 57.89 seconds (3357.89 seconds total)