Starting phenix.real_space_refine on Fri Aug 22 16:11:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8phw_17677/08_2025/8phw_17677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8phw_17677/08_2025/8phw_17677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2025/8phw_17677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2025/8phw_17677.map" model { file = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2025/8phw_17677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2025/8phw_17677.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 3500 2.51 5 N 847 2.21 5 O 976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5359 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3528 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 15, 'TRANS': 438} Chain breaks: 7 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 972 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'FY5': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.17, per 1000 atoms: 0.22 Number of scatterers: 5359 At special positions: 0 Unit cell: (87.72, 94.86, 104.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 976 8.00 N 847 7.00 C 3500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 133.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 46.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 27 through 52 removed outlier: 3.742A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.860A pdb=" N PHE A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 117 removed outlier: 4.217A pdb=" N GLY A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.612A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.718A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.743A pdb=" N LEU A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.891A pdb=" N MET A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.153A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 257 through 274 removed outlier: 4.055A pdb=" N ASN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.595A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.875A pdb=" N GLY A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 removed outlier: 3.522A pdb=" N ALA A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 527 through 559 removed outlier: 3.685A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 597 Proline residue: A 588 - end of helix Processing helix chain 'A' and resid 617 through 646 removed outlier: 3.665A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 435 removed outlier: 7.052A pdb=" N SER A 434 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A 520 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 removed outlier: 4.208A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 54 removed outlier: 6.837A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.777A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.777A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 822 1.32 - 1.45: 1624 1.45 - 1.57: 2991 1.57 - 1.70: 1 1.70 - 1.82: 53 Bond restraints: 5491 Sorted by residual: bond pdb=" O20 FY5 A 701 " pdb=" S21 FY5 A 701 " ideal model delta sigma weight residual 1.673 1.603 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C THR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.331 1.351 -0.020 7.90e-03 1.60e+04 6.28e+00 bond pdb=" C18 FY5 A 701 " pdb=" O20 FY5 A 701 " ideal model delta sigma weight residual 1.372 1.421 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" N VAL L 34 " pdb=" CA VAL L 34 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.25e-02 6.40e+03 2.09e+00 bond pdb=" C SER H 36 " pdb=" N ILE H 37 " ideal model delta sigma weight residual 1.334 1.316 0.017 1.24e-02 6.50e+03 1.98e+00 ... (remaining 5486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 7000 1.36 - 2.72: 372 2.72 - 4.07: 56 4.07 - 5.43: 18 5.43 - 6.79: 6 Bond angle restraints: 7452 Sorted by residual: angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 112.83 108.67 4.16 9.90e-01 1.02e+00 1.77e+01 angle pdb=" N TYR H 63 " pdb=" CA TYR H 63 " pdb=" C TYR H 63 " ideal model delta sigma weight residual 108.34 112.26 -3.92 1.31e+00 5.83e-01 8.93e+00 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " pdb=" CG TYR A 590 " ideal model delta sigma weight residual 113.90 119.01 -5.11 1.80e+00 3.09e-01 8.05e+00 angle pdb=" C ASN A 403 " pdb=" CA ASN A 403 " pdb=" CB ASN A 403 " ideal model delta sigma weight residual 110.42 115.50 -5.08 1.99e+00 2.53e-01 6.51e+00 ... (remaining 7447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.98: 2818 11.98 - 23.96: 279 23.96 - 35.94: 111 35.94 - 47.92: 36 47.92 - 59.90: 11 Dihedral angle restraints: 3255 sinusoidal: 1292 harmonic: 1963 Sorted by residual: dihedral pdb=" CA CYS A 607 " pdb=" C CYS A 607 " pdb=" N GLY A 608 " pdb=" CA GLY A 608 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLY A 608 " pdb=" C GLY A 608 " pdb=" N THR A 609 " pdb=" CA THR A 609 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASN A 617 " pdb=" C ASN A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 3252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 496 0.029 - 0.058: 229 0.058 - 0.087: 76 0.087 - 0.115: 37 0.115 - 0.144: 9 Chirality restraints: 847 Sorted by residual: chirality pdb=" CA VAL A 473 " pdb=" N VAL A 473 " pdb=" C VAL A 473 " pdb=" CB VAL A 473 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA THR A 186 " pdb=" N THR A 186 " pdb=" C THR A 186 " pdb=" CB THR A 186 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA PRO A 220 " pdb=" N PRO A 220 " pdb=" C PRO A 220 " pdb=" CB PRO A 220 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 844 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 219 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO A 220 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 106 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 107 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 107 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 107 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 590 " -0.013 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR A 590 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 590 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 590 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 590 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 590 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 590 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 590 " -0.001 2.00e-02 2.50e+03 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 793 2.75 - 3.29: 5508 3.29 - 3.82: 8421 3.82 - 4.36: 9687 4.36 - 4.90: 16556 Nonbonded interactions: 40965 Sorted by model distance: nonbonded pdb=" O CYS A 101 " pdb=" OG SER A 269 " model vdw 2.209 3.040 nonbonded pdb=" O ALA A 415 " pdb=" OG SER A 418 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG H 70 " pdb=" O SER H 88 " model vdw 2.248 3.120 nonbonded pdb=" O CYS A 474 " pdb=" N ALA A 519 " model vdw 2.252 3.120 ... (remaining 40960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.190 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 0.070 5497 Z= 0.233 Angle : 0.723 6.790 7464 Z= 0.423 Chirality : 0.041 0.144 847 Planarity : 0.005 0.058 905 Dihedral : 12.284 59.901 1991 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 6.20 % Allowed : 7.75 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.26), residues: 669 helix: -1.77 (0.25), residues: 283 sheet: -1.50 (0.57), residues: 81 loop : -3.36 (0.26), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 70 TYR 0.025 0.002 TYR A 590 PHE 0.010 0.001 PHE A 537 TRP 0.014 0.002 TRP A 254 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 5491) covalent geometry : angle 0.72217 ( 7452) SS BOND : bond 0.00428 ( 6) SS BOND : angle 1.12052 ( 12) hydrogen bonds : bond 0.13904 ( 256) hydrogen bonds : angle 5.86732 ( 750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6160 (ttp80) REVERT: A 170 MET cc_start: 0.7729 (ttm) cc_final: 0.7378 (ttm) REVERT: A 218 ILE cc_start: 0.7663 (mm) cc_final: 0.7459 (tt) REVERT: A 253 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6436 (mtm110) REVERT: A 386 PHE cc_start: 0.8258 (t80) cc_final: 0.7730 (t80) REVERT: A 390 MET cc_start: 0.7207 (mtm) cc_final: 0.6897 (mtm) REVERT: A 417 MET cc_start: 0.6765 (mmm) cc_final: 0.6395 (mmm) REVERT: A 601 LYS cc_start: 0.7751 (tttp) cc_final: 0.7317 (tttp) REVERT: A 631 MET cc_start: 0.6745 (tpp) cc_final: 0.6223 (tpp) REVERT: H 32 PHE cc_start: 0.8359 (t80) cc_final: 0.8126 (t80) REVERT: L 18 ASP cc_start: 0.5539 (m-30) cc_final: 0.5334 (m-30) REVERT: L 43 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7601 (mmtm) outliers start: 36 outliers final: 16 residues processed: 167 average time/residue: 0.0574 time to fit residues: 12.7499 Evaluate side-chains 147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123870 restraints weight = 9194.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127853 restraints weight = 4467.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.130443 restraints weight = 2732.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132085 restraints weight = 1941.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133276 restraints weight = 1537.033| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5497 Z= 0.145 Angle : 0.608 7.504 7464 Z= 0.313 Chirality : 0.042 0.274 847 Planarity : 0.005 0.058 905 Dihedral : 8.144 58.629 886 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 6.20 % Allowed : 14.80 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.30), residues: 669 helix: 0.24 (0.29), residues: 296 sheet: -1.04 (0.60), residues: 78 loop : -2.74 (0.29), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.015 0.001 TYR A 625 PHE 0.022 0.001 PHE A 73 TRP 0.009 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5491) covalent geometry : angle 0.60663 ( 7452) SS BOND : bond 0.00428 ( 6) SS BOND : angle 1.24349 ( 12) hydrogen bonds : bond 0.04846 ( 256) hydrogen bonds : angle 4.54287 ( 750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.7684 (ttm) cc_final: 0.7459 (ttm) REVERT: A 173 TYR cc_start: 0.7482 (m-80) cc_final: 0.7239 (m-80) REVERT: A 217 MET cc_start: 0.7929 (mmp) cc_final: 0.7514 (mmp) REVERT: A 253 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6592 (mtm110) REVERT: A 386 PHE cc_start: 0.8097 (t80) cc_final: 0.7404 (t80) REVERT: A 390 MET cc_start: 0.7115 (mtm) cc_final: 0.6793 (mtm) REVERT: A 417 MET cc_start: 0.6643 (mmm) cc_final: 0.6327 (mmm) REVERT: A 533 LYS cc_start: 0.7948 (mttm) cc_final: 0.7695 (mttm) REVERT: A 545 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7875 (mm) REVERT: A 601 LYS cc_start: 0.7622 (tttp) cc_final: 0.7222 (tttp) REVERT: A 631 MET cc_start: 0.6756 (tpp) cc_final: 0.6236 (tpp) REVERT: H 32 PHE cc_start: 0.8303 (t80) cc_final: 0.8066 (t80) REVERT: L 18 ASP cc_start: 0.6019 (m-30) cc_final: 0.5705 (m-30) REVERT: L 43 LYS cc_start: 0.7706 (mmtm) cc_final: 0.7497 (mmtm) outliers start: 36 outliers final: 19 residues processed: 157 average time/residue: 0.0550 time to fit residues: 11.8673 Evaluate side-chains 147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 59 optimal weight: 7.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 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 = 0.3891 r_free = 0.3891 target = 0.145427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126042 restraints weight = 9132.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129782 restraints weight = 4558.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132272 restraints weight = 2842.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133727 restraints weight = 2039.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.134881 restraints weight = 1644.893| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5497 Z= 0.136 Angle : 0.591 7.455 7464 Z= 0.301 Chirality : 0.041 0.167 847 Planarity : 0.004 0.042 905 Dihedral : 7.242 58.374 877 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 6.37 % Allowed : 17.73 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.32), residues: 669 helix: 0.99 (0.31), residues: 296 sheet: -0.95 (0.60), residues: 83 loop : -2.45 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.014 0.001 TYR L 50 PHE 0.014 0.001 PHE A 73 TRP 0.009 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5491) covalent geometry : angle 0.58968 ( 7452) SS BOND : bond 0.00415 ( 6) SS BOND : angle 1.10120 ( 12) hydrogen bonds : bond 0.04460 ( 256) hydrogen bonds : angle 4.32686 ( 750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6240 (ttp80) REVERT: A 173 TYR cc_start: 0.7396 (m-80) cc_final: 0.7183 (m-80) REVERT: A 217 MET cc_start: 0.7890 (mmp) cc_final: 0.7636 (mmp) REVERT: A 253 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7166 (mtm110) REVERT: A 386 PHE cc_start: 0.8009 (t80) cc_final: 0.7277 (t80) REVERT: A 390 MET cc_start: 0.7028 (mtm) cc_final: 0.6725 (mtm) REVERT: A 404 THR cc_start: 0.6330 (OUTLIER) cc_final: 0.6047 (m) REVERT: A 533 LYS cc_start: 0.7885 (mttm) cc_final: 0.7651 (mttm) REVERT: A 545 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 601 LYS cc_start: 0.7468 (tttp) cc_final: 0.7106 (tttp) REVERT: A 631 MET cc_start: 0.6727 (tpp) cc_final: 0.6234 (tpp) REVERT: L 43 LYS cc_start: 0.7658 (mmtm) cc_final: 0.7458 (mmtm) outliers start: 37 outliers final: 27 residues processed: 155 average time/residue: 0.0603 time to fit residues: 12.5463 Evaluate side-chains 161 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 25 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 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 = 0.3895 r_free = 0.3895 target = 0.145906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126484 restraints weight = 9055.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130192 restraints weight = 4560.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132638 restraints weight = 2861.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134119 restraints weight = 2063.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135181 restraints weight = 1668.225| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5497 Z= 0.147 Angle : 0.600 7.733 7464 Z= 0.302 Chirality : 0.041 0.157 847 Planarity : 0.004 0.043 905 Dihedral : 6.985 60.443 875 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 6.71 % Allowed : 18.76 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.32), residues: 669 helix: 1.21 (0.31), residues: 296 sheet: -0.84 (0.60), residues: 83 loop : -2.42 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.016 0.001 TYR L 50 PHE 0.014 0.001 PHE A 73 TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5491) covalent geometry : angle 0.59862 ( 7452) SS BOND : bond 0.00622 ( 6) SS BOND : angle 1.22905 ( 12) hydrogen bonds : bond 0.04349 ( 256) hydrogen bonds : angle 4.27912 ( 750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6257 (ttp80) REVERT: A 173 TYR cc_start: 0.7356 (m-80) cc_final: 0.7142 (m-80) REVERT: A 217 MET cc_start: 0.7956 (mmp) cc_final: 0.7728 (mmp) REVERT: A 253 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7081 (mtm110) REVERT: A 386 PHE cc_start: 0.7954 (t80) cc_final: 0.7266 (t80) REVERT: A 390 MET cc_start: 0.6999 (mtm) cc_final: 0.6736 (mtm) REVERT: A 404 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.6028 (m) REVERT: A 533 LYS cc_start: 0.7876 (mttm) cc_final: 0.7662 (mttm) REVERT: A 545 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7883 (mm) REVERT: A 601 LYS cc_start: 0.7428 (tttp) cc_final: 0.7084 (tttp) REVERT: A 631 MET cc_start: 0.6722 (tpp) cc_final: 0.6234 (tpp) REVERT: L 43 LYS cc_start: 0.7655 (mmtm) cc_final: 0.7407 (mmtm) REVERT: L 97 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6158 (mm) outliers start: 39 outliers final: 26 residues processed: 155 average time/residue: 0.0544 time to fit residues: 11.3301 Evaluate side-chains 157 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.0070 chunk 65 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 49 optimal weight: 0.3980 chunk 41 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.0010 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 0.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.149597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130487 restraints weight = 9151.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134299 restraints weight = 4504.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.136862 restraints weight = 2768.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138509 restraints weight = 1961.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139636 restraints weight = 1538.291| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5497 Z= 0.097 Angle : 0.555 7.890 7464 Z= 0.275 Chirality : 0.039 0.137 847 Planarity : 0.004 0.041 905 Dihedral : 6.552 62.618 874 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.65 % Allowed : 20.83 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.33), residues: 669 helix: 1.57 (0.31), residues: 296 sheet: -0.38 (0.62), residues: 78 loop : -2.31 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.013 0.001 TYR A 239 PHE 0.017 0.001 PHE H 32 TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 5491) covalent geometry : angle 0.55443 ( 7452) SS BOND : bond 0.00408 ( 6) SS BOND : angle 0.78849 ( 12) hydrogen bonds : bond 0.03449 ( 256) hydrogen bonds : angle 3.92590 ( 750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.7937 (mmp) cc_final: 0.7727 (mmp) REVERT: A 390 MET cc_start: 0.6987 (mtm) cc_final: 0.6754 (mtm) REVERT: A 545 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7851 (mm) REVERT: A 601 LYS cc_start: 0.7088 (tttp) cc_final: 0.6820 (tttp) REVERT: A 631 MET cc_start: 0.6746 (tpp) cc_final: 0.6285 (tpp) REVERT: L 43 LYS cc_start: 0.7560 (mmtm) cc_final: 0.7358 (mmtm) REVERT: L 97 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6099 (mm) outliers start: 27 outliers final: 16 residues processed: 149 average time/residue: 0.0508 time to fit residues: 10.4372 Evaluate side-chains 148 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 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 365 GLN A 445 ASN A 544 ASN H 42 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126072 restraints weight = 9079.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129908 restraints weight = 4458.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.132474 restraints weight = 2756.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134087 restraints weight = 1965.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135225 restraints weight = 1559.341| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5497 Z= 0.159 Angle : 0.613 7.710 7464 Z= 0.306 Chirality : 0.042 0.167 847 Planarity : 0.004 0.043 905 Dihedral : 6.387 61.747 865 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.16 % Allowed : 20.65 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.33), residues: 669 helix: 1.52 (0.31), residues: 293 sheet: -0.63 (0.59), residues: 83 loop : -2.26 (0.32), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 614 TYR 0.020 0.001 TYR L 50 PHE 0.018 0.001 PHE H 32 TRP 0.011 0.001 TRP A 254 HIS 0.002 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5491) covalent geometry : angle 0.61116 ( 7452) SS BOND : bond 0.00662 ( 6) SS BOND : angle 1.33525 ( 12) hydrogen bonds : bond 0.04272 ( 256) hydrogen bonds : angle 4.14895 ( 750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.198 Fit side-chains REVERT: A 173 TYR cc_start: 0.7370 (m-80) cc_final: 0.7156 (m-80) REVERT: A 217 MET cc_start: 0.8025 (mmp) cc_final: 0.7793 (mmp) REVERT: A 253 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6957 (mtm110) REVERT: A 386 PHE cc_start: 0.7914 (t80) cc_final: 0.7324 (t80) REVERT: A 390 MET cc_start: 0.7056 (mtm) cc_final: 0.6789 (mtm) REVERT: A 533 LYS cc_start: 0.7900 (mttm) cc_final: 0.7497 (mttm) REVERT: A 545 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7849 (mm) REVERT: A 601 LYS cc_start: 0.7414 (tttp) cc_final: 0.7045 (tttp) REVERT: A 631 MET cc_start: 0.6824 (tpp) cc_final: 0.6307 (tpp) REVERT: L 43 LYS cc_start: 0.7643 (mmtm) cc_final: 0.7402 (mmtm) REVERT: L 97 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6227 (mm) outliers start: 30 outliers final: 22 residues processed: 150 average time/residue: 0.0546 time to fit residues: 11.3427 Evaluate side-chains 155 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.0170 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 38 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN ** L 7 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 = 0.3912 r_free = 0.3912 target = 0.147117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127665 restraints weight = 9164.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131518 restraints weight = 4536.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134090 restraints weight = 2799.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135628 restraints weight = 1981.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136744 restraints weight = 1572.095| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5497 Z= 0.117 Angle : 0.583 7.442 7464 Z= 0.290 Chirality : 0.040 0.150 847 Planarity : 0.004 0.044 905 Dihedral : 6.241 62.660 865 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.65 % Allowed : 21.34 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.33), residues: 669 helix: 1.57 (0.31), residues: 296 sheet: -0.32 (0.61), residues: 78 loop : -2.24 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.012 0.001 TYR A 239 PHE 0.011 0.001 PHE A 276 TRP 0.007 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 5491) covalent geometry : angle 0.58121 ( 7452) SS BOND : bond 0.00505 ( 6) SS BOND : angle 1.19630 ( 12) hydrogen bonds : bond 0.03828 ( 256) hydrogen bonds : angle 4.00807 ( 750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.210 Fit side-chains REVERT: A 58 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6216 (ttp80) REVERT: A 386 PHE cc_start: 0.7850 (t80) cc_final: 0.7244 (t80) REVERT: A 390 MET cc_start: 0.6982 (mtm) cc_final: 0.6748 (mtm) REVERT: A 545 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 601 LYS cc_start: 0.7247 (tttp) cc_final: 0.6933 (tttp) REVERT: A 631 MET cc_start: 0.6766 (tpp) cc_final: 0.6295 (tpp) REVERT: H 42 GLN cc_start: 0.7645 (tt0) cc_final: 0.7334 (tt0) REVERT: L 43 LYS cc_start: 0.7600 (mmtm) cc_final: 0.7383 (mmtm) REVERT: L 97 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6182 (mm) outliers start: 27 outliers final: 18 residues processed: 146 average time/residue: 0.0570 time to fit residues: 11.2059 Evaluate side-chains 148 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 50 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 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 365 GLN ** L 7 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 = 0.3868 r_free = 0.3868 target = 0.144271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124332 restraints weight = 8940.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128207 restraints weight = 4466.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130765 restraints weight = 2778.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132464 restraints weight = 1981.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133300 restraints weight = 1562.223| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5497 Z= 0.184 Angle : 0.652 8.709 7464 Z= 0.327 Chirality : 0.043 0.169 847 Planarity : 0.004 0.046 905 Dihedral : 6.365 62.081 863 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.65 % Allowed : 21.51 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.32), residues: 669 helix: 1.36 (0.31), residues: 288 sheet: -0.25 (0.62), residues: 78 loop : -2.26 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 70 TYR 0.022 0.002 TYR L 50 PHE 0.019 0.001 PHE H 32 TRP 0.014 0.002 TRP A 254 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 5491) covalent geometry : angle 0.64967 ( 7452) SS BOND : bond 0.00751 ( 6) SS BOND : angle 1.60905 ( 12) hydrogen bonds : bond 0.04560 ( 256) hydrogen bonds : angle 4.26944 ( 750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.194 Fit side-chains REVERT: A 58 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6264 (ttp80) REVERT: A 217 MET cc_start: 0.8040 (mmp) cc_final: 0.7803 (mmp) REVERT: A 386 PHE cc_start: 0.7950 (t80) cc_final: 0.7288 (t80) REVERT: A 390 MET cc_start: 0.7096 (mtm) cc_final: 0.6810 (mtm) REVERT: A 545 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 601 LYS cc_start: 0.7449 (tttp) cc_final: 0.7064 (tttp) REVERT: A 631 MET cc_start: 0.6816 (tpp) cc_final: 0.6299 (tpp) REVERT: H 121 TYR cc_start: 0.7160 (m-80) cc_final: 0.6844 (m-80) REVERT: L 43 LYS cc_start: 0.7655 (mmtm) cc_final: 0.7402 (mmtm) REVERT: L 97 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6390 (mm) outliers start: 27 outliers final: 22 residues processed: 148 average time/residue: 0.0558 time to fit residues: 11.4549 Evaluate side-chains 156 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 12 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN ** L 7 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 = 0.3894 r_free = 0.3894 target = 0.146403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126678 restraints weight = 9067.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130560 restraints weight = 4472.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133118 restraints weight = 2753.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134639 restraints weight = 1956.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135828 restraints weight = 1563.221| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5497 Z= 0.127 Angle : 0.604 7.539 7464 Z= 0.300 Chirality : 0.041 0.140 847 Planarity : 0.004 0.046 905 Dihedral : 6.167 63.306 863 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.79 % Allowed : 22.20 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.32), residues: 669 helix: 1.51 (0.32), residues: 288 sheet: -0.28 (0.62), residues: 78 loop : -2.22 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.012 0.001 TYR L 50 PHE 0.010 0.001 PHE A 73 TRP 0.008 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5491) covalent geometry : angle 0.60288 ( 7452) SS BOND : bond 0.00505 ( 6) SS BOND : angle 1.19337 ( 12) hydrogen bonds : bond 0.03907 ( 256) hydrogen bonds : angle 4.04692 ( 750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.197 Fit side-chains REVERT: A 58 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6229 (ttp80) REVERT: A 386 PHE cc_start: 0.7896 (t80) cc_final: 0.7235 (t80) REVERT: A 390 MET cc_start: 0.7087 (mtm) cc_final: 0.6782 (mtm) REVERT: A 545 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7789 (mm) REVERT: A 601 LYS cc_start: 0.7260 (tttp) cc_final: 0.6911 (tttp) REVERT: A 631 MET cc_start: 0.6809 (tpp) cc_final: 0.6298 (tpp) REVERT: H 121 TYR cc_start: 0.7155 (m-80) cc_final: 0.6849 (m-80) REVERT: L 43 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7374 (mmtm) REVERT: L 97 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6349 (mm) outliers start: 22 outliers final: 18 residues processed: 143 average time/residue: 0.0581 time to fit residues: 11.2097 Evaluate side-chains 150 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 10 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 49 optimal weight: 0.0060 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN ** L 7 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 = 0.3923 r_free = 0.3923 target = 0.148164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.128293 restraints weight = 9092.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132173 restraints weight = 4480.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134622 restraints weight = 2765.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.136419 restraints weight = 1996.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.137590 restraints weight = 1548.347| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5497 Z= 0.117 Angle : 0.598 7.791 7464 Z= 0.297 Chirality : 0.041 0.176 847 Planarity : 0.004 0.045 905 Dihedral : 6.093 63.553 863 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.30 % Allowed : 22.55 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.32), residues: 669 helix: 1.51 (0.32), residues: 288 sheet: -0.27 (0.62), residues: 78 loop : -2.17 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.012 0.001 TYR L 50 PHE 0.024 0.001 PHE H 32 TRP 0.007 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 5491) covalent geometry : angle 0.59703 ( 7452) SS BOND : bond 0.00472 ( 6) SS BOND : angle 1.05883 ( 12) hydrogen bonds : bond 0.03768 ( 256) hydrogen bonds : angle 3.96520 ( 750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.165 Fit side-chains REVERT: A 58 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6219 (ttp80) REVERT: A 386 PHE cc_start: 0.7861 (t80) cc_final: 0.7228 (t80) REVERT: A 390 MET cc_start: 0.7021 (mtm) cc_final: 0.6761 (mtm) REVERT: A 545 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 601 LYS cc_start: 0.7174 (tttp) cc_final: 0.6859 (tttp) REVERT: A 631 MET cc_start: 0.6825 (tpp) cc_final: 0.6318 (tpp) REVERT: L 43 LYS cc_start: 0.7579 (mmtm) cc_final: 0.7356 (mmtm) REVERT: L 97 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6325 (mm) outliers start: 25 outliers final: 20 residues processed: 142 average time/residue: 0.0574 time to fit residues: 11.1724 Evaluate side-chains 147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.0070 chunk 13 optimal weight: 0.4980 chunk 58 optimal weight: 0.0060 chunk 22 optimal weight: 0.0370 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.2492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 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 = 0.3939 r_free = 0.3939 target = 0.149582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130051 restraints weight = 9086.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133919 restraints weight = 4515.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136394 restraints weight = 2787.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138063 restraints weight = 1992.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139070 restraints weight = 1567.579| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5497 Z= 0.106 Angle : 0.589 7.899 7464 Z= 0.292 Chirality : 0.040 0.170 847 Planarity : 0.004 0.043 905 Dihedral : 6.010 63.647 863 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.96 % Allowed : 22.55 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.33), residues: 669 helix: 1.55 (0.31), residues: 291 sheet: -0.20 (0.61), residues: 78 loop : -2.08 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 614 TYR 0.011 0.001 TYR A 239 PHE 0.025 0.001 PHE H 32 TRP 0.008 0.001 TRP A 470 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 5491) covalent geometry : angle 0.58791 ( 7452) SS BOND : bond 0.00404 ( 6) SS BOND : angle 1.02970 ( 12) hydrogen bonds : bond 0.03478 ( 256) hydrogen bonds : angle 3.84845 ( 750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1209.51 seconds wall clock time: 21 minutes 29.15 seconds (1289.15 seconds total)