Starting phenix.real_space_refine on Tue Feb 11 16:11:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9caj_45393/02_2025/9caj_45393_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9caj_45393/02_2025/9caj_45393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9caj_45393/02_2025/9caj_45393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9caj_45393/02_2025/9caj_45393.map" model { file = "/net/cci-nas-00/data/ceres_data/9caj_45393/02_2025/9caj_45393_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9caj_45393/02_2025/9caj_45393_neut.cif" } resolution = 3.51 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= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 9 5.49 5 S 39 5.16 5 C 3918 2.51 5 N 1079 2.21 5 O 1199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6245 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4840 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.77 Number of scatterers: 6245 At special positions: 0 Unit cell: (76.36, 87.15, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 39 16.00 P 9 15.00 O 1199 8.00 N 1079 7.00 C 3918 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: 1.56 Conformation dependent library (CDL) restraints added in 845.1 milliseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 41.1% alpha, 14.9% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 4.105A pdb=" N ILE A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 4.336A pdb=" N SER A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 157 through 165 removed outlier: 4.549A pdb=" N CYS A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 201 removed outlier: 3.706A pdb=" N SER A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.563A pdb=" N LEU A 207 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.708A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.682A pdb=" N ALA A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.714A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.718A pdb=" N TYR A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 495 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 551 Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.899A pdb=" N VAL A 556 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 removed outlier: 3.645A pdb=" N SER A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 600 removed outlier: 3.576A pdb=" N ASP A 598 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.967A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 32 through 43 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.232A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 41 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.232A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TRP A 115 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 7 " --> pdb=" O TRP A 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AA6, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.939A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS A 424 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 294 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A 426 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU A 292 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN A 428 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG A 290 " --> pdb=" O GLN A 428 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 430 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR A 288 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 432 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 530 Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.646A pdb=" N ASP B 134 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N LEU B 140 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 126 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2011 1.34 - 1.45: 886 1.45 - 1.57: 3415 1.57 - 1.69: 17 1.69 - 1.81: 61 Bond restraints: 6390 Sorted by residual: bond pdb=" N LYS A 10 " pdb=" CA LYS A 10 " ideal model delta sigma weight residual 1.453 1.480 -0.027 1.18e-02 7.18e+03 5.18e+00 bond pdb=" N ARG A 338 " pdb=" CA ARG A 338 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.46e-02 4.69e+03 4.75e+00 bond pdb=" N GLU A 340 " pdb=" CA GLU A 340 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.61e-02 3.86e+03 3.77e+00 bond pdb=" O3' DA C -1 " pdb=" P DC C 0 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.50e-02 4.44e+03 3.56e+00 bond pdb=" O3' DT C 4 " pdb=" P DA C 5 " ideal model delta sigma weight residual 1.607 1.580 0.027 1.50e-02 4.44e+03 3.36e+00 ... (remaining 6385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 8420 1.67 - 3.33: 205 3.33 - 5.00: 44 5.00 - 6.67: 11 6.67 - 8.34: 3 Bond angle restraints: 8683 Sorted by residual: angle pdb=" C4' DA C -1 " pdb=" C3' DA C -1 " pdb=" O3' DA C -1 " ideal model delta sigma weight residual 110.00 103.81 6.19 1.50e+00 4.44e-01 1.71e+01 angle pdb=" C LYS A 10 " pdb=" N PRO A 11 " pdb=" CA PRO A 11 " ideal model delta sigma weight residual 119.84 124.02 -4.18 1.25e+00 6.40e-01 1.12e+01 angle pdb=" C CYS A 109 " pdb=" N ASP A 110 " pdb=" CA ASP A 110 " ideal model delta sigma weight residual 121.54 127.52 -5.98 1.91e+00 2.74e-01 9.80e+00 angle pdb=" N GLY B 60 " pdb=" CA GLY B 60 " pdb=" C GLY B 60 " ideal model delta sigma weight residual 114.25 118.20 -3.95 1.30e+00 5.92e-01 9.23e+00 angle pdb=" O3' DT C 4 " pdb=" C3' DT C 4 " pdb=" C2' DT C 4 " ideal model delta sigma weight residual 111.50 107.00 4.50 1.50e+00 4.44e-01 9.00e+00 ... (remaining 8678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3408 17.97 - 35.94: 345 35.94 - 53.91: 76 53.91 - 71.88: 24 71.88 - 89.85: 9 Dihedral angle restraints: 3862 sinusoidal: 1628 harmonic: 2234 Sorted by residual: dihedral pdb=" CA VAL A 113 " pdb=" C VAL A 113 " pdb=" N LEU A 114 " pdb=" CA LEU A 114 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TYR A 111 " pdb=" C TYR A 111 " pdb=" N ILE A 112 " pdb=" CA ILE A 112 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ASP A 552 " pdb=" C ASP A 552 " pdb=" N ALA A 553 " pdb=" CA ALA A 553 " ideal model delta harmonic sigma weight residual 180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 756 0.047 - 0.093: 175 0.093 - 0.139: 39 0.139 - 0.186: 3 0.186 - 0.232: 1 Chirality restraints: 974 Sorted by residual: chirality pdb=" CB ILE A 435 " pdb=" CA ILE A 435 " pdb=" CG1 ILE A 435 " pdb=" CG2 ILE A 435 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C3' DT C 4 " pdb=" C4' DT C 4 " pdb=" O3' DT C 4 " pdb=" C2' DT C 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA VAL A 4 " pdb=" N VAL A 4 " pdb=" C VAL A 4 " pdb=" CB VAL A 4 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 971 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 436 " -0.055 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 437 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 456 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 457 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 53 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO B 54 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.023 5.00e-02 4.00e+02 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 83 2.65 - 3.21: 5753 3.21 - 3.78: 9333 3.78 - 4.34: 12421 4.34 - 4.90: 20680 Nonbonded interactions: 48270 Sorted by model distance: nonbonded pdb=" OE2 GLU A 9 " pdb=" OD2 ASP A 117 " model vdw 2.088 3.040 nonbonded pdb=" OE2 GLU A 9 " pdb="MN MN A 701 " model vdw 2.124 2.320 nonbonded pdb=" OP1 DA C 5 " pdb="MN MN A 701 " model vdw 2.151 2.320 nonbonded pdb=" OG SER A 289 " pdb=" OG1 THR A 430 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 204 " pdb=" OD1 ASP A 604 " model vdw 2.296 3.040 ... (remaining 48265 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 group one per residue 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: 3.150 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.650 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 0.004 0.065 6390 Z= 0.237 Angle : 0.663 8.336 8683 Z= 0.360 Chirality : 0.042 0.232 974 Planarity : 0.005 0.085 1091 Dihedral : 15.919 89.853 2420 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.45 % Allowed : 0.60 % Favored : 98.95 % 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: -0.25 (0.31), residues: 769 helix: 1.05 (0.30), residues: 293 sheet: -0.50 (0.45), residues: 148 loop : -1.07 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.007 0.001 HIS B 156 PHE 0.011 0.001 PHE B 52 TYR 0.014 0.001 TYR A 240 ARG 0.003 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7068 (mm) cc_final: 0.6852 (mm) REVERT: A 40 GLU cc_start: 0.7154 (mp0) cc_final: 0.6868 (mp0) REVERT: A 164 MET cc_start: 0.6093 (mpp) cc_final: 0.5565 (mpp) REVERT: A 185 ASP cc_start: 0.7013 (t70) cc_final: 0.6666 (t0) REVERT: A 198 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7618 (mtmm) REVERT: A 243 LEU cc_start: 0.8216 (tp) cc_final: 0.7955 (tt) REVERT: A 282 GLU cc_start: 0.6430 (mp0) cc_final: 0.5844 (mp0) REVERT: A 380 LYS cc_start: 0.7601 (mppt) cc_final: 0.7380 (mppt) REVERT: A 386 ASP cc_start: 0.6972 (t70) cc_final: 0.6572 (t70) REVERT: B 33 VAL cc_start: 0.8196 (t) cc_final: 0.7853 (m) outliers start: 3 outliers final: 0 residues processed: 171 average time/residue: 0.2123 time to fit residues: 46.2597 Evaluate side-chains 156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.0010 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 172 HIS A 357 GLN ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111382 restraints weight = 9429.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114513 restraints weight = 4167.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116516 restraints weight = 2257.198| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6390 Z= 0.236 Angle : 0.582 10.734 8683 Z= 0.293 Chirality : 0.041 0.155 974 Planarity : 0.005 0.064 1091 Dihedral : 12.108 88.990 932 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % Rotamer: Outliers : 0.75 % Allowed : 11.38 % Favored : 87.87 % 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: -0.27 (0.31), residues: 769 helix: 1.00 (0.30), residues: 298 sheet: -0.56 (0.44), residues: 151 loop : -1.07 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 14 HIS 0.007 0.001 HIS A 29 PHE 0.012 0.002 PHE A 127 TYR 0.013 0.001 TYR A 240 ARG 0.006 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7123 (mm) cc_final: 0.6851 (mm) REVERT: A 40 GLU cc_start: 0.7307 (mp0) cc_final: 0.6880 (mp0) REVERT: A 162 ASN cc_start: 0.6165 (m110) cc_final: 0.5833 (m110) REVERT: A 185 ASP cc_start: 0.7045 (t70) cc_final: 0.6794 (t70) REVERT: A 198 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7626 (mtmm) REVERT: A 243 LEU cc_start: 0.8298 (tp) cc_final: 0.7941 (tt) REVERT: A 327 ARG cc_start: 0.6316 (tmt170) cc_final: 0.6032 (tmt170) REVERT: A 380 LYS cc_start: 0.7637 (mppt) cc_final: 0.7429 (mppt) REVERT: A 386 ASP cc_start: 0.6841 (t70) cc_final: 0.6563 (t70) outliers start: 5 outliers final: 3 residues processed: 174 average time/residue: 0.2175 time to fit residues: 47.9428 Evaluate side-chains 163 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 289 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109160 restraints weight = 9682.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112335 restraints weight = 4349.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114359 restraints weight = 2373.565| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 0.043 6390 Z= 0.269 Angle : 0.593 8.891 8683 Z= 0.299 Chirality : 0.042 0.156 974 Planarity : 0.004 0.044 1091 Dihedral : 11.856 88.999 932 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.20 % Favored : 94.67 % Rotamer: Outliers : 1.95 % Allowed : 14.37 % 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: -0.29 (0.31), residues: 769 helix: 1.01 (0.30), residues: 298 sheet: -0.61 (0.45), residues: 151 loop : -1.09 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 29 PHE 0.023 0.002 PHE A 45 TYR 0.011 0.001 TYR A 578 ARG 0.004 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7237 (mm) cc_final: 0.6999 (mm) REVERT: A 33 ASN cc_start: 0.7927 (p0) cc_final: 0.7695 (p0) REVERT: A 40 GLU cc_start: 0.7371 (mp0) cc_final: 0.6927 (mp0) REVERT: A 158 THR cc_start: 0.6846 (OUTLIER) cc_final: 0.6222 (t) REVERT: A 162 ASN cc_start: 0.6144 (m110) cc_final: 0.5589 (m110) REVERT: A 185 ASP cc_start: 0.6949 (t70) cc_final: 0.6724 (t70) REVERT: A 198 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7643 (mtmm) REVERT: A 251 LYS cc_start: 0.6330 (OUTLIER) cc_final: 0.5969 (pttt) REVERT: A 327 ARG cc_start: 0.6343 (tmt170) cc_final: 0.6031 (tmt170) REVERT: A 380 LYS cc_start: 0.7645 (mppt) cc_final: 0.7425 (mppt) REVERT: A 386 ASP cc_start: 0.6847 (t70) cc_final: 0.6607 (t70) outliers start: 13 outliers final: 5 residues processed: 164 average time/residue: 0.2179 time to fit residues: 45.7907 Evaluate side-chains 161 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain B residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 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 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108051 restraints weight = 9754.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111323 restraints weight = 4335.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113360 restraints weight = 2353.413| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6390 Z= 0.285 Angle : 0.591 8.108 8683 Z= 0.297 Chirality : 0.042 0.158 974 Planarity : 0.004 0.039 1091 Dihedral : 11.811 88.366 932 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 3.59 % Allowed : 14.07 % Favored : 82.34 % 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: -0.31 (0.31), residues: 769 helix: 1.01 (0.30), residues: 299 sheet: -0.63 (0.45), residues: 151 loop : -1.09 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 29 PHE 0.028 0.002 PHE A 45 TYR 0.012 0.001 TYR A 578 ARG 0.003 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7298 (mm) cc_final: 0.7093 (mm) REVERT: A 40 GLU cc_start: 0.7407 (mp0) cc_final: 0.6940 (mp0) REVERT: A 162 ASN cc_start: 0.6058 (m110) cc_final: 0.5712 (m110) REVERT: A 198 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7690 (mtmm) REVERT: A 243 LEU cc_start: 0.8201 (tp) cc_final: 0.7887 (tt) REVERT: A 362 TYR cc_start: 0.7348 (m-10) cc_final: 0.7131 (m-80) REVERT: A 380 LYS cc_start: 0.7641 (mppt) cc_final: 0.7427 (mppt) REVERT: A 386 ASP cc_start: 0.6823 (t70) cc_final: 0.6557 (t70) REVERT: B 93 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8199 (ttp80) REVERT: B 95 LEU cc_start: 0.7951 (mt) cc_final: 0.7728 (mt) outliers start: 24 outliers final: 18 residues processed: 172 average time/residue: 0.2180 time to fit residues: 47.8091 Evaluate side-chains 181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.0050 chunk 7 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109870 restraints weight = 9673.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113070 restraints weight = 4367.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115091 restraints weight = 2390.382| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6390 Z= 0.213 Angle : 0.566 7.571 8683 Z= 0.286 Chirality : 0.040 0.150 974 Planarity : 0.004 0.036 1091 Dihedral : 11.654 87.745 932 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 3.14 % Allowed : 15.72 % Favored : 81.14 % 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: -0.23 (0.31), residues: 769 helix: 1.06 (0.30), residues: 299 sheet: -0.61 (0.45), residues: 151 loop : -1.02 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 39 PHE 0.016 0.001 PHE A 127 TYR 0.010 0.001 TYR A 411 ARG 0.006 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7221 (mm) cc_final: 0.6970 (mm) REVERT: A 40 GLU cc_start: 0.7362 (mp0) cc_final: 0.7009 (mp0) REVERT: A 158 THR cc_start: 0.6869 (OUTLIER) cc_final: 0.6263 (t) REVERT: A 162 ASN cc_start: 0.6020 (m110) cc_final: 0.5478 (m110) REVERT: A 185 ASP cc_start: 0.6853 (t70) cc_final: 0.6574 (t70) REVERT: A 198 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7632 (mtmm) REVERT: A 243 LEU cc_start: 0.8188 (tp) cc_final: 0.7873 (tt) REVERT: A 282 GLU cc_start: 0.6337 (mp0) cc_final: 0.5955 (mp0) REVERT: A 386 ASP cc_start: 0.6843 (t70) cc_final: 0.6597 (t70) outliers start: 21 outliers final: 14 residues processed: 175 average time/residue: 0.2267 time to fit residues: 49.5893 Evaluate side-chains 169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 53 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107845 restraints weight = 9602.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111058 restraints weight = 4298.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113030 restraints weight = 2343.907| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6390 Z= 0.327 Angle : 0.621 8.388 8683 Z= 0.314 Chirality : 0.043 0.218 974 Planarity : 0.004 0.061 1091 Dihedral : 11.731 87.192 932 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.94 % Favored : 94.93 % Rotamer: Outliers : 3.74 % Allowed : 17.07 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.31), residues: 769 helix: 0.99 (0.30), residues: 299 sheet: -0.58 (0.46), residues: 149 loop : -1.07 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.011 0.001 HIS A 60 PHE 0.031 0.002 PHE A 45 TYR 0.012 0.001 TYR A 578 ARG 0.006 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7363 (mm) cc_final: 0.7154 (mm) REVERT: A 40 GLU cc_start: 0.7400 (mp0) cc_final: 0.6961 (mp0) REVERT: A 158 THR cc_start: 0.6882 (OUTLIER) cc_final: 0.6236 (t) REVERT: A 159 ASP cc_start: 0.8076 (m-30) cc_final: 0.7876 (m-30) REVERT: A 162 ASN cc_start: 0.6056 (m110) cc_final: 0.5516 (m110) REVERT: A 198 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7649 (mtmm) REVERT: A 243 LEU cc_start: 0.8204 (tp) cc_final: 0.7877 (tt) REVERT: A 362 TYR cc_start: 0.7357 (m-10) cc_final: 0.6803 (m-80) REVERT: A 386 ASP cc_start: 0.6845 (t70) cc_final: 0.6582 (t70) REVERT: B 64 LYS cc_start: 0.8005 (mppt) cc_final: 0.7780 (mppt) REVERT: B 93 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8005 (ttp80) REVERT: B 114 MET cc_start: 0.7596 (mmp) cc_final: 0.7334 (mmm) outliers start: 25 outliers final: 18 residues processed: 177 average time/residue: 0.2103 time to fit residues: 47.0328 Evaluate side-chains 186 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107139 restraints weight = 9677.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110351 restraints weight = 4323.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112390 restraints weight = 2349.980| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6390 Z= 0.342 Angle : 0.625 9.193 8683 Z= 0.316 Chirality : 0.043 0.181 974 Planarity : 0.004 0.054 1091 Dihedral : 11.766 86.771 932 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 3.89 % Allowed : 17.37 % Favored : 78.74 % 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: -0.42 (0.31), residues: 769 helix: 0.82 (0.30), residues: 306 sheet: -0.64 (0.45), residues: 156 loop : -1.13 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 60 PHE 0.026 0.002 PHE A 45 TYR 0.012 0.001 TYR A 426 ARG 0.005 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7398 (mp0) cc_final: 0.6907 (mp0) REVERT: A 158 THR cc_start: 0.6850 (OUTLIER) cc_final: 0.6251 (t) REVERT: A 162 ASN cc_start: 0.6036 (m110) cc_final: 0.5511 (m110) REVERT: A 198 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7683 (mtmm) REVERT: A 243 LEU cc_start: 0.8202 (tp) cc_final: 0.7883 (tt) REVERT: A 362 TYR cc_start: 0.7358 (m-10) cc_final: 0.7145 (m-80) REVERT: A 386 ASP cc_start: 0.6885 (t70) cc_final: 0.6612 (t70) REVERT: B 64 LYS cc_start: 0.8006 (mppt) cc_final: 0.7785 (mppt) REVERT: B 93 ARG cc_start: 0.8479 (ttp80) cc_final: 0.7936 (ttp80) REVERT: B 114 MET cc_start: 0.7597 (mmp) cc_final: 0.7344 (mmm) outliers start: 26 outliers final: 21 residues processed: 180 average time/residue: 0.2112 time to fit residues: 48.3653 Evaluate side-chains 184 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107446 restraints weight = 9626.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110653 restraints weight = 4292.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112668 restraints weight = 2332.183| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6390 Z= 0.311 Angle : 0.636 8.799 8683 Z= 0.317 Chirality : 0.042 0.171 974 Planarity : 0.004 0.052 1091 Dihedral : 11.746 86.342 932 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.81 % Favored : 95.06 % Rotamer: Outliers : 3.89 % Allowed : 17.66 % Favored : 78.44 % 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: -0.46 (0.31), residues: 769 helix: 0.79 (0.30), residues: 306 sheet: -0.60 (0.46), residues: 149 loop : -1.19 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS B 156 PHE 0.024 0.002 PHE A 45 TYR 0.011 0.001 TYR A 578 ARG 0.008 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 HIS cc_start: 0.7225 (t-170) cc_final: 0.6760 (t70) REVERT: A 40 GLU cc_start: 0.7385 (mp0) cc_final: 0.6962 (mp0) REVERT: A 158 THR cc_start: 0.6831 (OUTLIER) cc_final: 0.6282 (t) REVERT: A 162 ASN cc_start: 0.5999 (m110) cc_final: 0.5549 (m110) REVERT: A 198 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7731 (mtmm) REVERT: A 362 TYR cc_start: 0.7343 (m-10) cc_final: 0.7133 (m-80) REVERT: A 386 ASP cc_start: 0.6884 (t70) cc_final: 0.6604 (t70) REVERT: B 64 LYS cc_start: 0.8008 (mppt) cc_final: 0.7774 (mppt) REVERT: B 93 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8030 (ttp-170) REVERT: B 114 MET cc_start: 0.7574 (mmp) cc_final: 0.7315 (mmm) outliers start: 26 outliers final: 22 residues processed: 173 average time/residue: 0.2217 time to fit residues: 48.6269 Evaluate side-chains 185 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 76 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108570 restraints weight = 9689.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111871 restraints weight = 4331.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113922 restraints weight = 2341.074| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6390 Z= 0.228 Angle : 0.617 8.969 8683 Z= 0.308 Chirality : 0.041 0.159 974 Planarity : 0.004 0.050 1091 Dihedral : 11.661 85.956 932 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 3.44 % Allowed : 19.31 % Favored : 77.25 % 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: -0.24 (0.31), residues: 769 helix: 0.96 (0.30), residues: 299 sheet: -0.69 (0.46), residues: 156 loop : -0.88 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.004 0.001 HIS A 39 PHE 0.019 0.002 PHE A 45 TYR 0.010 0.001 TYR A 411 ARG 0.006 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 HIS cc_start: 0.7192 (t-170) cc_final: 0.6749 (t70) REVERT: A 40 GLU cc_start: 0.7374 (mp0) cc_final: 0.6985 (mp0) REVERT: A 75 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8076 (mmmm) REVERT: A 158 THR cc_start: 0.6860 (OUTLIER) cc_final: 0.6307 (t) REVERT: A 162 ASN cc_start: 0.5981 (m110) cc_final: 0.5539 (m110) REVERT: A 198 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7638 (mtmm) REVERT: A 243 LEU cc_start: 0.8228 (tp) cc_final: 0.7934 (tt) REVERT: A 362 TYR cc_start: 0.7309 (m-10) cc_final: 0.7085 (m-80) REVERT: A 386 ASP cc_start: 0.6884 (t70) cc_final: 0.6596 (t70) REVERT: B 64 LYS cc_start: 0.7993 (mppt) cc_final: 0.7735 (mppt) REVERT: B 99 MET cc_start: 0.7995 (mtt) cc_final: 0.7748 (mtm) REVERT: B 114 MET cc_start: 0.7564 (mmp) cc_final: 0.7340 (mmm) outliers start: 23 outliers final: 15 residues processed: 174 average time/residue: 0.2177 time to fit residues: 48.1173 Evaluate side-chains 174 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.0000 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 46 optimal weight: 0.7980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109674 restraints weight = 9678.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112930 restraints weight = 4311.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114962 restraints weight = 2343.094| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6390 Z= 0.202 Angle : 0.615 10.082 8683 Z= 0.305 Chirality : 0.041 0.155 974 Planarity : 0.004 0.069 1091 Dihedral : 11.603 85.915 932 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 2.84 % Allowed : 20.21 % Favored : 76.95 % 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: -0.21 (0.32), residues: 769 helix: 1.00 (0.30), residues: 300 sheet: -0.76 (0.45), residues: 158 loop : -0.84 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS B 156 PHE 0.016 0.002 PHE A 45 TYR 0.018 0.001 TYR A 41 ARG 0.006 0.000 ARG B 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.7809 (mt) cc_final: 0.7512 (mt) REVERT: A 29 HIS cc_start: 0.7141 (t-170) cc_final: 0.6747 (t70) REVERT: A 40 GLU cc_start: 0.7347 (mp0) cc_final: 0.6954 (mp0) REVERT: A 51 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7354 (ptm-80) REVERT: A 64 LEU cc_start: 0.8244 (tt) cc_final: 0.7932 (tp) REVERT: A 75 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8073 (mmmm) REVERT: A 158 THR cc_start: 0.6865 (OUTLIER) cc_final: 0.6271 (t) REVERT: A 162 ASN cc_start: 0.5942 (m110) cc_final: 0.5436 (m110) REVERT: A 198 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7599 (mtmm) REVERT: A 243 LEU cc_start: 0.8236 (tp) cc_final: 0.7919 (tt) REVERT: A 251 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5936 (pttt) REVERT: A 362 TYR cc_start: 0.7298 (m-10) cc_final: 0.7052 (m-80) REVERT: A 386 ASP cc_start: 0.6883 (t70) cc_final: 0.6605 (t70) REVERT: B 93 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8007 (ttp80) REVERT: B 99 MET cc_start: 0.7995 (mtt) cc_final: 0.7770 (mtm) REVERT: B 114 MET cc_start: 0.7562 (mmp) cc_final: 0.7322 (mmm) outliers start: 19 outliers final: 14 residues processed: 168 average time/residue: 0.2249 time to fit residues: 48.0470 Evaluate side-chains 178 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 0.0060 chunk 8 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109293 restraints weight = 9826.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112520 restraints weight = 4430.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114548 restraints weight = 2420.858| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6390 Z= 0.238 Angle : 0.616 9.642 8683 Z= 0.308 Chirality : 0.041 0.158 974 Planarity : 0.004 0.069 1091 Dihedral : 11.648 86.226 932 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.81 % Favored : 95.06 % Rotamer: Outliers : 3.14 % Allowed : 20.36 % Favored : 76.50 % 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: -0.19 (0.32), residues: 769 helix: 1.02 (0.30), residues: 300 sheet: -0.69 (0.46), residues: 150 loop : -0.87 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.006 0.001 HIS B 156 PHE 0.018 0.002 PHE A 45 TYR 0.055 0.002 TYR A 41 ARG 0.006 0.000 ARG B 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.07 seconds wall clock time: 43 minutes 7.54 seconds (2587.54 seconds total)