Starting phenix.real_space_refine on Tue Jun 10 04:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7a_28899/06_2025/8f7a_28899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7a_28899/06_2025/8f7a_28899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7a_28899/06_2025/8f7a_28899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7a_28899/06_2025/8f7a_28899.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7a_28899/06_2025/8f7a_28899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7a_28899/06_2025/8f7a_28899.cif" } resolution = 3.78 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5465 atoms to isotropic. 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 P 3 5.49 5 Mg 1 5.21 5 S 38 5.16 5 C 4335 2.51 5 N 1119 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6742 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5332 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 5327 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 683, 5327 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 5431 Chain: "B" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1377 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 6, 'TRANS': 162} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.90, per 1000 atoms: 1.17 Number of scatterers: 6742 At special positions: 0 Unit cell: (76.167, 97.092, 104.625, 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) S 38 16.00 P 3 15.00 Mg 1 11.99 O 1246 8.00 N 1119 7.00 C 4335 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: 2.10 Conformation dependent library (CDL) restraints added in 1.4 seconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 2 sheets defined 72.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.642A pdb=" N ASP A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.871A pdb=" N GLU A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 139 removed outlier: 3.790A pdb=" N TRP A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 4.071A pdb=" N MET A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 Processing helix chain 'A' and resid 181 through 199 Proline residue: A 187 - end of helix Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 204 through 229 Processing helix chain 'A' and resid 237 through 250 removed outlier: 3.527A pdb=" N GLN A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 279 Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.849A pdb=" N MET A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 309 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 329 through 344 Processing helix chain 'A' and resid 346 through 356 removed outlier: 4.301A pdb=" N SER A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 4.156A pdb=" N TYR A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 381 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 397 through 413 removed outlier: 3.566A pdb=" N PHE A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 438 removed outlier: 3.627A pdb=" N SER A 438 " --> pdb=" O GLN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 removed outlier: 4.125A pdb=" N HIS A 447 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 467 removed outlier: 3.810A pdb=" N ILE A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.537A pdb=" N ASN A 487 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 505 removed outlier: 3.624A pdb=" N LEU A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG A 504 " --> pdb=" O TRP A 500 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 510 through 523 Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 530 through 552 removed outlier: 3.717A pdb=" N LYS A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 559 removed outlier: 3.748A pdb=" N GLN A 558 " --> pdb=" O HIS A 555 " (cutoff:3.500A) Proline residue: A 559 - end of helix Processing helix chain 'A' and resid 560 through 573 Processing helix chain 'A' and resid 577 through 594 removed outlier: 4.402A pdb=" N GLU A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP A 594 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 616 removed outlier: 3.634A pdb=" N THR A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 605 " --> pdb=" O MET A 601 " (cutoff:3.500A) Proline residue: A 607 - end of helix Processing helix chain 'A' and resid 619 through 635 removed outlier: 3.677A pdb=" N GLN A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 639 through 657 Proline residue: A 649 - end of helix Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.537A pdb=" N ILE A 690 " --> pdb=" O SER A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.955A pdb=" N LYS B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 102' Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.343A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 172 Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.715A pdb=" N LEU B 15 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 65 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 67 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 48 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.715A pdb=" N LEU B 15 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2152 1.34 - 1.46: 1293 1.46 - 1.57: 3379 1.57 - 1.69: 5 1.69 - 1.81: 60 Bond restraints: 6889 Sorted by residual: bond pdb=" CA TRP B 66 " pdb=" CB TRP B 66 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.51e-02 4.39e+03 1.77e+00 bond pdb=" CA THR B 137 " pdb=" CB THR B 137 " ideal model delta sigma weight residual 1.534 1.513 0.021 1.78e-02 3.16e+03 1.36e+00 bond pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta sigma weight residual 1.466 1.452 0.015 1.36e-02 5.41e+03 1.16e+00 bond pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 1.528 1.514 0.014 1.33e-02 5.65e+03 1.07e+00 bond pdb=" CB TRP B 66 " pdb=" CG TRP B 66 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 ... (remaining 6884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 9062 1.57 - 3.14: 251 3.14 - 4.71: 43 4.71 - 6.27: 15 6.27 - 7.84: 5 Bond angle restraints: 9376 Sorted by residual: angle pdb=" C THR B 139 " pdb=" N PHE B 140 " pdb=" CA PHE B 140 " ideal model delta sigma weight residual 122.09 116.56 5.53 1.79e+00 3.12e-01 9.53e+00 angle pdb=" N ILE A 237 " pdb=" CA ILE A 237 " pdb=" C ILE A 237 " ideal model delta sigma weight residual 109.34 115.13 -5.79 2.08e+00 2.31e-01 7.74e+00 angle pdb=" N LYS B 136 " pdb=" CA LYS B 136 " pdb=" C LYS B 136 " ideal model delta sigma weight residual 113.01 109.68 3.33 1.20e+00 6.94e-01 7.70e+00 angle pdb=" C1' GTP B 302 " pdb=" O4' GTP B 302 " pdb=" C4' GTP B 302 " ideal model delta sigma weight residual 111.80 103.96 7.84 3.00e+00 1.11e-01 6.83e+00 angle pdb=" C2' GTP B 302 " pdb=" C1' GTP B 302 " pdb=" N9 GTP B 302 " ideal model delta sigma weight residual 109.47 117.16 -7.69 3.00e+00 1.11e-01 6.57e+00 ... (remaining 9371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3730 17.52 - 35.03: 283 35.03 - 52.55: 93 52.55 - 70.06: 26 70.06 - 87.58: 7 Dihedral angle restraints: 4139 sinusoidal: 1631 harmonic: 2508 Sorted by residual: dihedral pdb=" CA ASN B 158 " pdb=" C ASN B 158 " pdb=" N PHE B 159 " pdb=" CA PHE B 159 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 236 " pdb=" C LEU A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ALA A 143 " pdb=" C ALA A 143 " pdb=" N TRP A 144 " pdb=" CA TRP A 144 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 929 0.055 - 0.110: 160 0.110 - 0.165: 11 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1102 Sorted by residual: chirality pdb=" C1' GTP B 302 " pdb=" C2' GTP B 302 " pdb=" N9 GTP B 302 " pdb=" O4' GTP B 302 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2' GTP B 302 " pdb=" C1' GTP B 302 " pdb=" C3' GTP B 302 " pdb=" O2' GTP B 302 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" C3' GTP B 302 " pdb=" C2' GTP B 302 " pdb=" C4' GTP B 302 " pdb=" O3' GTP B 302 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1099 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 144 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 145 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 238 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 239 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 682 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO A 683 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 683 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 683 " 0.020 5.00e-02 4.00e+02 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 2 1.85 - 2.61: 123 2.61 - 3.37: 9904 3.37 - 4.14: 15648 4.14 - 4.90: 29120 Nonbonded interactions: 54797 Sorted by model distance: nonbonded pdb=" OG1 THR B 26 " pdb="MG MG B 301 " model vdw 1.085 2.170 nonbonded pdb="MG MG B 301 " pdb=" O3G GTP B 302 " model vdw 1.776 2.170 nonbonded pdb=" O PHE A 613 " pdb=" OG SER A 617 " model vdw 2.159 3.040 nonbonded pdb=" O PHE A 197 " pdb=" NH1 ARG A 208 " model vdw 2.162 3.120 nonbonded pdb=" OD2 ASP B 93 " pdb=" OG1 THR B 95 " model vdw 2.190 3.040 ... (remaining 54792 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=0.50 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: 136.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.210 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 : 0.005 0.046 6889 Z= 0.231 Angle : 0.692 7.842 9376 Z= 0.387 Chirality : 0.041 0.275 1102 Planarity : 0.004 0.042 1177 Dihedral : 15.306 87.575 2501 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 11.80 % Allowed : 9.50 % Favored : 78.70 % 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: -2.21 (0.27), residues: 843 helix: -0.71 (0.21), residues: 545 sheet: -4.45 (0.50), residues: 47 loop : -2.26 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 144 HIS 0.005 0.001 HIS B 32 PHE 0.014 0.001 PHE B 140 TYR 0.015 0.001 TYR B 148 ARG 0.003 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.16283 ( 398) hydrogen bonds : angle 6.73733 ( 1194) covalent geometry : bond 0.00517 ( 6889) covalent geometry : angle 0.69220 ( 9376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 223 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8358 (mt0) cc_final: 0.7927 (mt0) REVERT: A 182 MET cc_start: 0.8721 (ttp) cc_final: 0.8476 (ttt) REVERT: A 205 ILE cc_start: 0.8172 (pt) cc_final: 0.7760 (pt) REVERT: A 221 MET cc_start: 0.9070 (ttt) cc_final: 0.8648 (ttt) REVERT: A 279 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6878 (p90) REVERT: A 338 GLU cc_start: 0.7876 (tt0) cc_final: 0.7624 (tp30) REVERT: A 375 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7731 (mt) REVERT: A 499 LEU cc_start: 0.9111 (mt) cc_final: 0.8710 (mt) REVERT: A 515 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: A 516 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8190 (mt0) REVERT: A 541 ILE cc_start: 0.8711 (mt) cc_final: 0.8462 (mt) REVERT: A 683 PRO cc_start: 0.8166 (Cg_exo) cc_final: 0.7933 (Cg_endo) REVERT: A 717 LEU cc_start: 0.9214 (mm) cc_final: 0.8954 (mm) REVERT: A 720 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: B 91 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4141 (ttt) REVERT: B 131 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.3583 (mtm-85) REVERT: B 139 THR cc_start: 0.6653 (t) cc_final: 0.6382 (t) outliers start: 87 outliers final: 20 residues processed: 280 average time/residue: 0.1887 time to fit residues: 70.5987 Evaluate side-chains 174 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 384 GLN A 403 GLN A 414 GLN A 434 GLN A 447 HIS A 515 GLN A 644 GLN A 692 GLN A 712 ASN B 107 HIS B 116 ASN B 147 GLN B 156 ASN B 158 ASN B 175 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.085864 restraints weight = 19592.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089762 restraints weight = 10406.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.092342 restraints weight = 7163.126| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6889 Z= 0.170 Angle : 0.758 7.823 9376 Z= 0.386 Chirality : 0.045 0.271 1102 Planarity : 0.005 0.044 1177 Dihedral : 8.539 63.814 961 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.70 % Allowed : 20.08 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.29), residues: 843 helix: 0.67 (0.23), residues: 541 sheet: -3.53 (0.62), residues: 46 loop : -1.50 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 144 HIS 0.006 0.001 HIS A 137 PHE 0.027 0.002 PHE A 334 TYR 0.012 0.002 TYR B 100 ARG 0.006 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 398) hydrogen bonds : angle 4.86700 ( 1194) covalent geometry : bond 0.00366 ( 6889) covalent geometry : angle 0.75756 ( 9376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 214 ILE cc_start: 0.8341 (mt) cc_final: 0.7938 (mt) REVERT: A 221 MET cc_start: 0.8977 (ttt) cc_final: 0.8736 (ttt) REVERT: A 338 GLU cc_start: 0.8116 (tt0) cc_final: 0.7855 (tp30) REVERT: A 454 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 720 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: B 53 SER cc_start: 0.8798 (m) cc_final: 0.8530 (t) REVERT: B 160 GLU cc_start: 0.6954 (pt0) cc_final: 0.6693 (pm20) outliers start: 42 outliers final: 24 residues processed: 196 average time/residue: 0.1509 time to fit residues: 41.2996 Evaluate side-chains 166 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.122658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.088963 restraints weight = 26670.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092828 restraints weight = 12440.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094057 restraints weight = 7700.551| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 6889 Z= 0.168 Angle : 0.745 9.402 9376 Z= 0.372 Chirality : 0.045 0.286 1102 Planarity : 0.005 0.042 1177 Dihedral : 7.255 68.769 937 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.61 % Allowed : 22.25 % Favored : 73.13 % 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: -0.12 (0.29), residues: 843 helix: 0.87 (0.23), residues: 538 sheet: -3.62 (0.60), residues: 46 loop : -1.30 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 144 HIS 0.005 0.001 HIS A 341 PHE 0.013 0.001 PHE B 58 TYR 0.010 0.001 TYR B 148 ARG 0.006 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 398) hydrogen bonds : angle 4.67897 ( 1194) covalent geometry : bond 0.00392 ( 6889) covalent geometry : angle 0.74474 ( 9376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8770 (pt0) cc_final: 0.8350 (pt0) REVERT: A 97 ARG cc_start: 0.8328 (mmt90) cc_final: 0.7832 (mmt180) REVERT: A 193 MET cc_start: 0.8881 (tpp) cc_final: 0.8357 (tpp) REVERT: A 454 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 720 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: B 84 ASN cc_start: 0.8818 (m-40) cc_final: 0.8491 (m-40) REVERT: B 154 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7924 (mttm) REVERT: B 160 GLU cc_start: 0.7440 (pt0) cc_final: 0.7211 (pm20) outliers start: 34 outliers final: 20 residues processed: 164 average time/residue: 0.1643 time to fit residues: 37.3320 Evaluate side-chains 148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087666 restraints weight = 24532.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092092 restraints weight = 11187.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095132 restraints weight = 6671.618| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6889 Z= 0.144 Angle : 0.732 9.202 9376 Z= 0.360 Chirality : 0.044 0.269 1102 Planarity : 0.004 0.043 1177 Dihedral : 6.898 70.500 929 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.07 % Allowed : 24.42 % Favored : 71.51 % 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: 0.03 (0.30), residues: 843 helix: 0.90 (0.23), residues: 542 sheet: -3.13 (0.63), residues: 46 loop : -1.16 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 144 HIS 0.008 0.001 HIS A 475 PHE 0.026 0.001 PHE A 238 TYR 0.007 0.001 TYR B 100 ARG 0.007 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 398) hydrogen bonds : angle 4.53311 ( 1194) covalent geometry : bond 0.00323 ( 6889) covalent geometry : angle 0.73207 ( 9376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8813 (pt0) cc_final: 0.8342 (pt0) REVERT: A 80 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8911 (mm) REVERT: A 97 ARG cc_start: 0.8531 (mmt90) cc_final: 0.8063 (mmt180) REVERT: A 193 MET cc_start: 0.9007 (tpp) cc_final: 0.8793 (tpp) REVERT: A 205 ILE cc_start: 0.8407 (pt) cc_final: 0.8117 (pt) REVERT: A 212 VAL cc_start: 0.8758 (t) cc_final: 0.8235 (p) REVERT: A 221 MET cc_start: 0.8965 (ttt) cc_final: 0.8664 (ttt) REVERT: A 266 MET cc_start: 0.7683 (tmm) cc_final: 0.7401 (tmm) REVERT: A 267 GLU cc_start: 0.7863 (tp30) cc_final: 0.7640 (tp30) REVERT: A 329 PHE cc_start: 0.8255 (t80) cc_final: 0.7927 (t80) REVERT: A 720 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7580 (m-80) REVERT: B 32 HIS cc_start: 0.7791 (m-70) cc_final: 0.7476 (m-70) REVERT: B 84 ASN cc_start: 0.8849 (m-40) cc_final: 0.8545 (m-40) outliers start: 30 outliers final: 19 residues processed: 153 average time/residue: 0.1648 time to fit residues: 34.4758 Evaluate side-chains 140 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088817 restraints weight = 19381.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.092103 restraints weight = 9838.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094697 restraints weight = 6800.202| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6889 Z= 0.154 Angle : 0.732 11.010 9376 Z= 0.359 Chirality : 0.044 0.260 1102 Planarity : 0.004 0.041 1177 Dihedral : 6.802 70.169 928 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.34 % Allowed : 22.66 % Favored : 73.00 % 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: 0.20 (0.29), residues: 843 helix: 1.05 (0.23), residues: 541 sheet: -2.67 (0.66), residues: 45 loop : -1.22 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 144 HIS 0.008 0.001 HIS A 475 PHE 0.015 0.001 PHE A 279 TYR 0.009 0.001 TYR B 148 ARG 0.006 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 398) hydrogen bonds : angle 4.45597 ( 1194) covalent geometry : bond 0.00352 ( 6889) covalent geometry : angle 0.73173 ( 9376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.9050 (tpp) cc_final: 0.8791 (tpp) REVERT: A 205 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8344 (pt) REVERT: A 216 THR cc_start: 0.8680 (m) cc_final: 0.8410 (p) REVERT: A 227 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6328 (tm-30) REVERT: A 266 MET cc_start: 0.7921 (tmm) cc_final: 0.7643 (tmm) REVERT: A 279 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6921 (p90) REVERT: A 329 PHE cc_start: 0.8230 (t80) cc_final: 0.7882 (t80) REVERT: A 720 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: B 32 HIS cc_start: 0.7933 (m-70) cc_final: 0.7567 (m-70) REVERT: B 67 ASP cc_start: 0.8953 (t0) cc_final: 0.8734 (t0) REVERT: B 74 PHE cc_start: 0.8284 (m-10) cc_final: 0.7757 (m-80) outliers start: 32 outliers final: 17 residues processed: 141 average time/residue: 0.1724 time to fit residues: 33.8926 Evaluate side-chains 136 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.124219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091803 restraints weight = 20635.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094688 restraints weight = 10585.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095473 restraints weight = 7297.820| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6889 Z= 0.137 Angle : 0.721 9.162 9376 Z= 0.349 Chirality : 0.044 0.283 1102 Planarity : 0.004 0.043 1177 Dihedral : 6.674 68.366 927 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.26 % Allowed : 24.42 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.29), residues: 843 helix: 1.20 (0.23), residues: 533 sheet: -2.18 (0.70), residues: 45 loop : -1.35 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 144 HIS 0.004 0.001 HIS A 341 PHE 0.027 0.002 PHE A 56 TYR 0.014 0.001 TYR A 84 ARG 0.008 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 398) hydrogen bonds : angle 4.37941 ( 1194) covalent geometry : bond 0.00313 ( 6889) covalent geometry : angle 0.72142 ( 9376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.872 Fit side-chains REVERT: A 51 GLU cc_start: 0.8861 (pt0) cc_final: 0.8429 (pt0) REVERT: A 172 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 193 MET cc_start: 0.9022 (tpp) cc_final: 0.8764 (tpp) REVERT: A 205 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8413 (pt) REVERT: A 213 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8214 (mt-10) REVERT: A 216 THR cc_start: 0.8771 (m) cc_final: 0.8387 (p) REVERT: A 266 MET cc_start: 0.7868 (tmm) cc_final: 0.7575 (tmm) REVERT: A 329 PHE cc_start: 0.8153 (t80) cc_final: 0.7795 (t80) REVERT: A 429 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8260 (mm) REVERT: A 720 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: B 32 HIS cc_start: 0.7720 (m-70) cc_final: 0.7290 (m-70) REVERT: B 74 PHE cc_start: 0.8225 (m-10) cc_final: 0.7930 (m-80) REVERT: B 91 MET cc_start: 0.8143 (tpp) cc_final: 0.7934 (tpp) outliers start: 24 outliers final: 17 residues processed: 133 average time/residue: 0.2028 time to fit residues: 37.8567 Evaluate side-chains 127 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085962 restraints weight = 17607.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.088003 restraints weight = 9606.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089218 restraints weight = 7389.523| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6889 Z= 0.226 Angle : 0.782 8.914 9376 Z= 0.389 Chirality : 0.048 0.303 1102 Planarity : 0.004 0.040 1177 Dihedral : 6.878 63.438 925 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.34 % Allowed : 24.29 % Favored : 71.37 % 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: -0.11 (0.29), residues: 843 helix: 0.95 (0.22), residues: 538 sheet: -2.34 (0.68), residues: 45 loop : -1.76 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 144 HIS 0.005 0.001 HIS A 59 PHE 0.019 0.002 PHE A 238 TYR 0.018 0.002 TYR B 148 ARG 0.007 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 398) hydrogen bonds : angle 4.73986 ( 1194) covalent geometry : bond 0.00537 ( 6889) covalent geometry : angle 0.78179 ( 9376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.752 Fit side-chains REVERT: A 213 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8147 (mt-10) REVERT: A 216 THR cc_start: 0.8910 (m) cc_final: 0.8512 (p) REVERT: A 225 MET cc_start: 0.8539 (ttt) cc_final: 0.8306 (ttm) REVERT: A 227 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6315 (tm-30) REVERT: A 266 MET cc_start: 0.8217 (tmm) cc_final: 0.7910 (tmm) REVERT: A 368 MET cc_start: 0.8617 (mmm) cc_final: 0.8273 (mtp) REVERT: A 429 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8502 (mm) REVERT: A 634 SER cc_start: 0.9459 (m) cc_final: 0.9098 (p) REVERT: A 720 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: B 32 HIS cc_start: 0.8184 (m-70) cc_final: 0.7743 (m-70) REVERT: B 74 PHE cc_start: 0.8747 (m-10) cc_final: 0.8487 (m-80) REVERT: B 127 ASP cc_start: 0.5822 (OUTLIER) cc_final: 0.5563 (m-30) outliers start: 32 outliers final: 21 residues processed: 134 average time/residue: 0.1567 time to fit residues: 29.6410 Evaluate side-chains 128 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088263 restraints weight = 20773.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091790 restraints weight = 10565.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.092721 restraints weight = 7142.769| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.7883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6889 Z= 0.143 Angle : 0.743 10.107 9376 Z= 0.361 Chirality : 0.045 0.291 1102 Planarity : 0.004 0.043 1177 Dihedral : 6.583 71.587 925 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.12 % Allowed : 25.64 % Favored : 71.23 % 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: 0.06 (0.29), residues: 843 helix: 1.09 (0.22), residues: 537 sheet: -2.42 (0.66), residues: 50 loop : -1.67 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 144 HIS 0.004 0.001 HIS A 447 PHE 0.021 0.001 PHE A 56 TYR 0.007 0.001 TYR B 157 ARG 0.008 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 398) hydrogen bonds : angle 4.43833 ( 1194) covalent geometry : bond 0.00328 ( 6889) covalent geometry : angle 0.74269 ( 9376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.763 Fit side-chains REVERT: A 95 LYS cc_start: 0.8705 (tptt) cc_final: 0.8486 (mtpt) REVERT: A 205 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8656 (pp) REVERT: A 216 THR cc_start: 0.8776 (m) cc_final: 0.8372 (p) REVERT: A 225 MET cc_start: 0.8628 (ttt) cc_final: 0.8424 (ttm) REVERT: A 266 MET cc_start: 0.8122 (tmm) cc_final: 0.7796 (tmm) REVERT: A 291 LEU cc_start: 0.7982 (tt) cc_final: 0.7706 (tt) REVERT: A 368 MET cc_start: 0.8525 (mmm) cc_final: 0.8155 (mtp) REVERT: A 628 ASP cc_start: 0.8540 (m-30) cc_final: 0.8232 (t0) REVERT: A 634 SER cc_start: 0.9408 (m) cc_final: 0.9093 (p) REVERT: A 720 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: B 32 HIS cc_start: 0.8002 (m-70) cc_final: 0.7497 (m-70) REVERT: B 74 PHE cc_start: 0.8586 (m-10) cc_final: 0.8311 (m-80) outliers start: 23 outliers final: 17 residues processed: 135 average time/residue: 0.1615 time to fit residues: 30.5418 Evaluate side-chains 122 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 0.4980 chunk 59 optimal weight: 0.0060 chunk 72 optimal weight: 0.7980 chunk 69 optimal weight: 0.0170 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 overall best weight: 0.4434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.091183 restraints weight = 19818.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094083 restraints weight = 10020.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096217 restraints weight = 7256.421| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6889 Z= 0.137 Angle : 0.755 12.001 9376 Z= 0.364 Chirality : 0.046 0.390 1102 Planarity : 0.004 0.041 1177 Dihedral : 6.338 75.124 925 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.99 % Allowed : 26.19 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.29), residues: 843 helix: 1.07 (0.22), residues: 540 sheet: -1.98 (0.69), residues: 50 loop : -1.62 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 144 HIS 0.004 0.001 HIS A 341 PHE 0.018 0.001 PHE A 56 TYR 0.008 0.001 TYR B 157 ARG 0.008 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 398) hydrogen bonds : angle 4.42789 ( 1194) covalent geometry : bond 0.00306 ( 6889) covalent geometry : angle 0.75472 ( 9376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.928 Fit side-chains REVERT: A 193 MET cc_start: 0.9100 (tpp) cc_final: 0.8807 (tpp) REVERT: A 216 THR cc_start: 0.8788 (m) cc_final: 0.8395 (p) REVERT: A 266 MET cc_start: 0.8059 (tmm) cc_final: 0.7720 (tmm) REVERT: A 291 LEU cc_start: 0.7925 (tt) cc_final: 0.7684 (tt) REVERT: A 329 PHE cc_start: 0.8120 (t80) cc_final: 0.7712 (t80) REVERT: A 368 MET cc_start: 0.8567 (mmm) cc_final: 0.8095 (mtp) REVERT: A 628 ASP cc_start: 0.8394 (m-30) cc_final: 0.8153 (t0) REVERT: A 634 SER cc_start: 0.9497 (m) cc_final: 0.9118 (p) REVERT: A 720 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: B 32 HIS cc_start: 0.7827 (m-70) cc_final: 0.7373 (m-70) REVERT: B 74 PHE cc_start: 0.8493 (m-10) cc_final: 0.8291 (m-80) outliers start: 22 outliers final: 15 residues processed: 133 average time/residue: 0.1523 time to fit residues: 28.3346 Evaluate side-chains 122 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 447 HIS ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088654 restraints weight = 24947.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092211 restraints weight = 12090.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.093076 restraints weight = 7882.847| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.8237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6889 Z= 0.146 Angle : 0.767 11.680 9376 Z= 0.371 Chirality : 0.047 0.425 1102 Planarity : 0.004 0.042 1177 Dihedral : 6.214 74.743 921 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.31 % Allowed : 26.59 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.29), residues: 843 helix: 0.96 (0.22), residues: 549 sheet: -1.50 (0.71), residues: 47 loop : -1.64 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 144 HIS 0.008 0.001 HIS A 703 PHE 0.018 0.001 PHE A 56 TYR 0.018 0.001 TYR A 203 ARG 0.007 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 398) hydrogen bonds : angle 4.47453 ( 1194) covalent geometry : bond 0.00338 ( 6889) covalent geometry : angle 0.76673 ( 9376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.723 Fit side-chains REVERT: A 193 MET cc_start: 0.9123 (tpp) cc_final: 0.8828 (tpp) REVERT: A 216 THR cc_start: 0.8801 (m) cc_final: 0.8416 (p) REVERT: A 266 MET cc_start: 0.8096 (tmm) cc_final: 0.7745 (tmm) REVERT: A 291 LEU cc_start: 0.7981 (tt) cc_final: 0.7725 (tt) REVERT: A 368 MET cc_start: 0.8580 (mmm) cc_final: 0.8124 (mtp) REVERT: A 628 ASP cc_start: 0.8414 (m-30) cc_final: 0.8162 (t0) REVERT: A 634 SER cc_start: 0.9497 (m) cc_final: 0.9115 (p) REVERT: A 703 HIS cc_start: 0.7763 (m90) cc_final: 0.7488 (m90) REVERT: A 720 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: B 32 HIS cc_start: 0.7871 (m-70) cc_final: 0.7391 (m-70) REVERT: B 74 PHE cc_start: 0.8580 (m-10) cc_final: 0.8354 (m-80) outliers start: 17 outliers final: 15 residues processed: 121 average time/residue: 0.1633 time to fit residues: 27.5254 Evaluate side-chains 120 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 0.0270 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.122215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088639 restraints weight = 19719.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.091695 restraints weight = 9897.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.093657 restraints weight = 7205.691| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.8384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6889 Z= 0.155 Angle : 0.772 11.726 9376 Z= 0.373 Chirality : 0.047 0.428 1102 Planarity : 0.004 0.043 1177 Dihedral : 6.219 74.307 921 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.12 % Allowed : 26.05 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.29), residues: 843 helix: 0.97 (0.22), residues: 550 sheet: -1.48 (0.71), residues: 47 loop : -1.57 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 144 HIS 0.008 0.001 HIS A 703 PHE 0.017 0.001 PHE A 56 TYR 0.017 0.001 TYR A 203 ARG 0.006 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 398) hydrogen bonds : angle 4.50862 ( 1194) covalent geometry : bond 0.00364 ( 6889) covalent geometry : angle 0.77215 ( 9376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3077.92 seconds wall clock time: 55 minutes 8.78 seconds (3308.78 seconds total)