Starting phenix.real_space_refine on Sun Dec 29 20:24:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7a_28899/12_2024/8f7a_28899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7a_28899/12_2024/8f7a_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_28899/12_2024/8f7a_28899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7a_28899/12_2024/8f7a_28899.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7a_28899/12_2024/8f7a_28899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7a_28899/12_2024/8f7a_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.64, per 1000 atoms: 0.98 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: 2.00 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: 0.61 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: 1.85 Time building geometry restraints manager: 2.25 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.180 Find NCS groups from input model: 0.060 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- 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= 0.332 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 *********************** 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 : 0.741 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: 0.1795 time to fit residues: 66.9900 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 : 0.835 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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= 0.231 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 *********************** 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 : 0.764 Fit side-chains revert: symmetry clash REVERT: A 214 ILE cc_start: 0.8356 (mt) cc_final: 0.7949 (mt) REVERT: A 221 MET cc_start: 0.8997 (ttt) cc_final: 0.8760 (ttt) REVERT: A 338 GLU cc_start: 0.8356 (tt0) cc_final: 0.7840 (tp30) REVERT: A 454 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8093 (mm) REVERT: A 720 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: B 53 SER cc_start: 0.8883 (m) cc_final: 0.8603 (t) REVERT: B 64 ASP cc_start: 0.7114 (m-30) cc_final: 0.6894 (m-30) REVERT: B 87 CYS cc_start: 0.8100 (p) cc_final: 0.7883 (p) REVERT: B 160 GLU cc_start: 0.6977 (pt0) cc_final: 0.6630 (pm20) outliers start: 42 outliers final: 24 residues processed: 196 average time/residue: 0.1627 time to fit residues: 44.4030 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 : 0.748 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6889 Z= 0.241 Angle : 0.746 9.516 9376 Z= 0.373 Chirality : 0.045 0.286 1102 Planarity : 0.005 0.042 1177 Dihedral : 7.255 69.544 937 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.02 % Allowed : 21.71 % Favored : 73.27 % 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: -3.57 (0.61), residues: 46 loop : -1.30 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 144 HIS 0.005 0.001 HIS A 137 PHE 0.013 0.001 PHE B 58 TYR 0.009 0.001 TYR B 148 ARG 0.006 0.001 ARG A 104 *********************** 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 183 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8896 (pt0) cc_final: 0.8366 (pt0) REVERT: A 97 ARG cc_start: 0.8255 (mmt90) cc_final: 0.7748 (mmt180) REVERT: A 193 MET cc_start: 0.8971 (tpp) cc_final: 0.8421 (tpp) REVERT: A 338 GLU cc_start: 0.8627 (tt0) cc_final: 0.8136 (tp30) REVERT: A 454 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8252 (mm) REVERT: A 585 GLU cc_start: 0.8588 (tt0) cc_final: 0.8321 (tt0) REVERT: A 720 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: B 53 SER cc_start: 0.8952 (m) cc_final: 0.8752 (t) REVERT: B 84 ASN cc_start: 0.8873 (m-40) cc_final: 0.8467 (m-40) REVERT: B 154 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7774 (mttt) REVERT: B 160 GLU cc_start: 0.7474 (pt0) cc_final: 0.7112 (pm20) outliers start: 37 outliers final: 21 residues processed: 168 average time/residue: 0.1703 time to fit residues: 39.1237 Evaluate side-chains 150 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 579 VAL 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 49 VAL Chi-restraints excluded: chain B residue 111 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 75 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6889 Z= 0.218 Angle : 0.731 9.245 9376 Z= 0.362 Chirality : 0.044 0.263 1102 Planarity : 0.004 0.043 1177 Dihedral : 6.907 70.321 929 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.93 % Allowed : 24.42 % Favored : 71.64 % 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: -0.01 (0.29), residues: 843 helix: 0.88 (0.23), residues: 541 sheet: -3.13 (0.64), residues: 45 loop : -1.21 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 144 HIS 0.005 0.001 HIS A 341 PHE 0.026 0.001 PHE A 238 TYR 0.007 0.001 TYR B 148 ARG 0.008 0.001 ARG A 40 *********************** 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 158 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8920 (pt0) cc_final: 0.8412 (pt0) REVERT: A 97 ARG cc_start: 0.8570 (mmt90) cc_final: 0.8089 (mmt180) REVERT: A 172 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8374 (mm-30) REVERT: A 193 MET cc_start: 0.9075 (tpp) cc_final: 0.8829 (tpp) REVERT: A 199 MET cc_start: 0.7633 (tpp) cc_final: 0.7321 (tpp) REVERT: A 221 MET cc_start: 0.9015 (ttt) cc_final: 0.8707 (ttt) REVERT: A 266 MET cc_start: 0.7576 (tmm) cc_final: 0.7281 (tmm) REVERT: A 329 PHE cc_start: 0.8071 (t80) cc_final: 0.7727 (t80) REVERT: A 338 GLU cc_start: 0.8677 (tt0) cc_final: 0.8312 (tp30) REVERT: A 585 GLU cc_start: 0.8665 (tt0) cc_final: 0.8285 (tt0) REVERT: A 625 LEU cc_start: 0.8194 (mm) cc_final: 0.7990 (mm) REVERT: A 720 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: B 26 THR cc_start: 0.8885 (m) cc_final: 0.8679 (p) REVERT: B 32 HIS cc_start: 0.7883 (m-70) cc_final: 0.7510 (m-70) REVERT: B 84 ASN cc_start: 0.8908 (m-40) cc_final: 0.8464 (m-40) outliers start: 29 outliers final: 20 residues processed: 149 average time/residue: 0.1737 time to fit residues: 35.4126 Evaluate side-chains 139 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 113 LEU Chi-restraints excluded: chain A residue 124 VAL 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 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL 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 52 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 87 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 0 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.6522 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= 0.205 Angle : 0.718 11.571 9376 Z= 0.353 Chirality : 0.043 0.158 1102 Planarity : 0.004 0.041 1177 Dihedral : 6.766 71.447 928 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.66 % Allowed : 24.29 % Favored : 72.05 % 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: 0.22 (0.29), residues: 843 helix: 1.11 (0.23), residues: 536 sheet: -2.72 (0.66), residues: 45 loop : -1.28 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 144 HIS 0.009 0.001 HIS A 475 PHE 0.031 0.001 PHE B 37 TYR 0.007 0.001 TYR B 148 ARG 0.005 0.001 ARG A 40 *********************** 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 150 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8955 (pt0) cc_final: 0.8495 (pt0) REVERT: A 172 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8399 (mm-30) REVERT: A 193 MET cc_start: 0.9124 (tpp) cc_final: 0.8839 (tpp) REVERT: A 205 ILE cc_start: 0.8676 (pt) cc_final: 0.8369 (pt) REVERT: A 212 VAL cc_start: 0.8960 (t) cc_final: 0.8753 (p) REVERT: A 227 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6288 (tm-30) REVERT: A 266 MET cc_start: 0.7626 (tmm) cc_final: 0.7289 (tmm) REVERT: A 329 PHE cc_start: 0.7877 (t80) cc_final: 0.7518 (t80) REVERT: A 338 GLU cc_start: 0.8706 (tt0) cc_final: 0.8402 (tp30) REVERT: A 429 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 585 GLU cc_start: 0.8679 (tt0) cc_final: 0.8296 (tt0) REVERT: A 720 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: B 32 HIS cc_start: 0.7911 (m-70) cc_final: 0.7442 (m-70) REVERT: B 74 PHE cc_start: 0.8120 (m-10) cc_final: 0.7787 (m-80) REVERT: B 84 ASN cc_start: 0.8904 (m-40) cc_final: 0.8469 (m-40) outliers start: 27 outliers final: 17 residues processed: 143 average time/residue: 0.1674 time to fit residues: 32.8910 Evaluate side-chains 135 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 227 GLU Chi-restraints excluded: chain A residue 262 SER 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 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 87 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6889 Z= 0.263 Angle : 0.759 9.377 9376 Z= 0.372 Chirality : 0.045 0.241 1102 Planarity : 0.004 0.044 1177 Dihedral : 6.837 67.223 927 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.88 % Allowed : 23.47 % Favored : 71.64 % 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: -0.00 (0.29), residues: 843 helix: 1.04 (0.22), residues: 539 sheet: -2.82 (0.63), residues: 50 loop : -1.60 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 144 HIS 0.009 0.001 HIS A 475 PHE 0.016 0.001 PHE A 279 TYR 0.012 0.001 TYR B 148 ARG 0.007 0.001 ARG A 40 *********************** 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 152 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.782 Fit side-chains REVERT: A 172 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8580 (mm-30) REVERT: A 216 THR cc_start: 0.8757 (m) cc_final: 0.8415 (p) REVERT: A 227 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6294 (tm-30) REVERT: A 266 MET cc_start: 0.7800 (tmm) cc_final: 0.7488 (tmm) REVERT: A 429 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8500 (mm) REVERT: A 585 GLU cc_start: 0.8765 (tt0) cc_final: 0.8413 (tt0) REVERT: A 628 ASP cc_start: 0.8812 (m-30) cc_final: 0.8331 (t0) REVERT: A 634 SER cc_start: 0.9386 (m) cc_final: 0.9075 (p) REVERT: A 720 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: B 32 HIS cc_start: 0.8176 (m-70) cc_final: 0.7673 (m-70) REVERT: B 74 PHE cc_start: 0.8539 (m-10) cc_final: 0.8198 (m-80) outliers start: 36 outliers final: 23 residues processed: 146 average time/residue: 0.1821 time to fit residues: 37.0082 Evaluate side-chains 128 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 78 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 261 ASP 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 429 LEU 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 676 THR Chi-restraints excluded: chain A residue 716 CYS 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 87 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.7592 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= 0.204 Angle : 0.739 11.162 9376 Z= 0.360 Chirality : 0.044 0.288 1102 Planarity : 0.004 0.040 1177 Dihedral : 6.599 73.632 927 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.66 % Allowed : 24.42 % Favored : 71.91 % 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: 1.12 (0.22), residues: 540 sheet: -2.39 (0.67), residues: 50 loop : -1.67 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 144 HIS 0.009 0.001 HIS A 475 PHE 0.021 0.001 PHE B 37 TYR 0.008 0.001 TYR B 157 ARG 0.007 0.001 ARG A 40 *********************** 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 148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.830 Fit side-chains REVERT: A 95 LYS cc_start: 0.8657 (tptt) cc_final: 0.8438 (mtmt) REVERT: A 216 THR cc_start: 0.8757 (m) cc_final: 0.8379 (p) REVERT: A 227 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6329 (tm-30) REVERT: A 266 MET cc_start: 0.7844 (tmm) cc_final: 0.7476 (tmm) REVERT: A 329 PHE cc_start: 0.7762 (t80) cc_final: 0.7379 (t80) REVERT: A 338 GLU cc_start: 0.8815 (tt0) cc_final: 0.8530 (tp30) REVERT: A 429 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8427 (mm) REVERT: A 448 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 451 MET cc_start: 0.8548 (mmm) cc_final: 0.8196 (mtt) REVERT: A 585 GLU cc_start: 0.8735 (tt0) cc_final: 0.8389 (tt0) REVERT: A 628 ASP cc_start: 0.8719 (m-30) cc_final: 0.8308 (t0) REVERT: A 634 SER cc_start: 0.9378 (m) cc_final: 0.9067 (p) REVERT: A 720 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: B 32 HIS cc_start: 0.8036 (m-70) cc_final: 0.7507 (m-70) REVERT: B 74 PHE cc_start: 0.8382 (m-10) cc_final: 0.8031 (m-80) outliers start: 27 outliers final: 21 residues processed: 141 average time/residue: 0.1657 time to fit residues: 32.0806 Evaluate side-chains 135 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 78 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 227 GLU 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 429 LEU 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 690 ILE Chi-restraints excluded: chain A residue 716 CYS 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 87 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 0.0070 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 0.0570 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.7800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6889 Z= 0.208 Angle : 0.740 11.841 9376 Z= 0.357 Chirality : 0.044 0.269 1102 Planarity : 0.004 0.041 1177 Dihedral : 6.415 74.539 927 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.99 % Allowed : 26.05 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.29), residues: 843 helix: 1.12 (0.23), residues: 540 sheet: -2.08 (0.68), residues: 50 loop : -1.62 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 144 HIS 0.004 0.001 HIS A 341 PHE 0.012 0.001 PHE B 58 TYR 0.010 0.001 TYR A 203 ARG 0.008 0.001 ARG A 40 *********************** 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: 22 poor density : 117 time to evaluate : 0.805 Fit side-chains REVERT: A 193 MET cc_start: 0.9135 (tpp) cc_final: 0.8900 (tpp) REVERT: A 216 THR cc_start: 0.8722 (m) cc_final: 0.8340 (p) REVERT: A 266 MET cc_start: 0.7780 (tmm) cc_final: 0.7372 (tmm) REVERT: A 329 PHE cc_start: 0.7730 (t80) cc_final: 0.7315 (t80) REVERT: A 338 GLU cc_start: 0.8802 (tt0) cc_final: 0.8552 (tp30) REVERT: A 429 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8446 (mm) REVERT: A 585 GLU cc_start: 0.8700 (tt0) cc_final: 0.8273 (tt0) REVERT: A 628 ASP cc_start: 0.8705 (m-30) cc_final: 0.8344 (t0) REVERT: A 634 SER cc_start: 0.9377 (m) cc_final: 0.9052 (p) REVERT: B 32 HIS cc_start: 0.7998 (m-70) cc_final: 0.7484 (m-70) REVERT: B 74 PHE cc_start: 0.8353 (m-10) cc_final: 0.8000 (m-80) outliers start: 22 outliers final: 19 residues processed: 134 average time/residue: 0.1727 time to fit residues: 32.0246 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 : 0.695 ------------------------------------------------------------------------------- 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 113 LEU Chi-restraints excluded: chain A residue 124 VAL 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 690 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 87 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6889 Z= 0.230 Angle : 0.752 12.417 9376 Z= 0.366 Chirality : 0.044 0.235 1102 Planarity : 0.004 0.043 1177 Dihedral : 6.101 74.044 923 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.26 % Allowed : 25.78 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 843 helix: 1.15 (0.23), residues: 539 sheet: -2.02 (0.68), residues: 50 loop : -1.54 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 144 HIS 0.004 0.001 HIS A 475 PHE 0.011 0.001 PHE B 58 TYR 0.009 0.001 TYR B 157 ARG 0.007 0.001 ARG A 40 *********************** 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 130 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.725 Fit side-chains REVERT: A 193 MET cc_start: 0.9158 (tpp) cc_final: 0.8801 (tpp) REVERT: A 216 THR cc_start: 0.8747 (m) cc_final: 0.8366 (p) REVERT: A 266 MET cc_start: 0.7871 (tmm) cc_final: 0.7444 (tmm) REVERT: A 329 PHE cc_start: 0.7784 (t80) cc_final: 0.7388 (t80) REVERT: A 338 GLU cc_start: 0.8833 (tt0) cc_final: 0.8574 (tp30) REVERT: A 585 GLU cc_start: 0.8730 (tt0) cc_final: 0.8360 (tt0) REVERT: A 628 ASP cc_start: 0.8692 (m-30) cc_final: 0.8326 (t0) REVERT: A 634 SER cc_start: 0.9388 (m) cc_final: 0.9075 (p) REVERT: B 32 HIS cc_start: 0.8096 (m-70) cc_final: 0.7522 (m-70) REVERT: B 74 PHE cc_start: 0.8458 (m-10) cc_final: 0.8100 (m-80) outliers start: 24 outliers final: 18 residues processed: 126 average time/residue: 0.1600 time to fit residues: 28.2984 Evaluate side-chains 119 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 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 690 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 87 CYS 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 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 51 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 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 75 GLN A 447 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.8125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6889 Z= 0.221 Angle : 0.756 12.427 9376 Z= 0.365 Chirality : 0.046 0.380 1102 Planarity : 0.004 0.044 1177 Dihedral : 5.960 74.348 919 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.99 % Allowed : 25.37 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 843 helix: 1.10 (0.23), residues: 543 sheet: -1.90 (0.68), residues: 50 loop : -1.49 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 144 HIS 0.003 0.001 HIS B 141 PHE 0.011 0.001 PHE B 58 TYR 0.009 0.001 TYR B 157 ARG 0.008 0.001 ARG A 40 ********************** 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 128 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.812 Fit side-chains REVERT: A 193 MET cc_start: 0.9153 (tpp) cc_final: 0.8794 (tpp) REVERT: A 216 THR cc_start: 0.8738 (m) cc_final: 0.8338 (p) REVERT: A 266 MET cc_start: 0.7898 (tmm) cc_final: 0.7467 (tmm) REVERT: A 291 LEU cc_start: 0.7735 (tt) cc_final: 0.7509 (tt) REVERT: A 329 PHE cc_start: 0.7718 (t80) cc_final: 0.7323 (t80) REVERT: A 585 GLU cc_start: 0.8734 (tt0) cc_final: 0.8362 (tt0) REVERT: A 628 ASP cc_start: 0.8685 (m-30) cc_final: 0.8317 (t0) REVERT: A 634 SER cc_start: 0.9374 (m) cc_final: 0.9067 (p) REVERT: B 32 HIS cc_start: 0.8088 (m-70) cc_final: 0.7497 (m-70) REVERT: B 74 PHE cc_start: 0.8483 (m-10) cc_final: 0.8157 (m-80) outliers start: 22 outliers final: 18 residues processed: 124 average time/residue: 0.1664 time to fit residues: 28.7576 Evaluate side-chains 119 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 269 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 690 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 87 CYS 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 61 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088452 restraints weight = 27099.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093586 restraints weight = 11939.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097280 restraints weight = 7057.589| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.8253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6889 Z= 0.209 Angle : 0.770 12.776 9376 Z= 0.370 Chirality : 0.046 0.425 1102 Planarity : 0.004 0.044 1177 Dihedral : 5.910 75.434 919 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.85 % Allowed : 26.05 % 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: 0.17 (0.29), residues: 843 helix: 1.04 (0.23), residues: 543 sheet: -1.74 (0.67), residues: 50 loop : -1.48 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 144 HIS 0.009 0.001 HIS A 703 PHE 0.012 0.001 PHE B 58 TYR 0.009 0.001 TYR B 157 ARG 0.008 0.001 ARG A 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.92 seconds wall clock time: 32 minutes 17.49 seconds (1937.49 seconds total)