Starting phenix.real_space_refine on Thu Nov 14 10:12:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/11_2024/8phw_17677.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/11_2024/8phw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/11_2024/8phw_17677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/11_2024/8phw_17677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/11_2024/8phw_17677.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/11_2024/8phw_17677.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 5.40, per 1000 atoms: 1.01 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: 1.30 Conformation dependent library (CDL) restraints added in 860.3 milliseconds 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: 0.55 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: 1.48 Time building geometry restraints manager: 1.54 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: 4.450 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.580 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- 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 5491 Z= 0.297 Angle : 0.722 6.790 7452 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP A 254 HIS 0.003 0.001 HIS A 115 PHE 0.010 0.001 PHE A 537 TYR 0.025 0.002 TYR A 590 ARG 0.003 0.000 ARG H 70 *********************** 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 : 0.571 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: 0.1531 time to fit residues: 33.7485 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 : 0.578 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.0040 chunk 27 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5491 Z= 0.183 Angle : 0.602 7.545 7452 Z= 0.310 Chirality : 0.042 0.297 847 Planarity : 0.005 0.057 905 Dihedral : 8.106 59.016 886 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.02 % Allowed : 14.46 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.30), residues: 669 helix: 0.23 (0.30), residues: 291 sheet: -1.02 (0.60), residues: 78 loop : -2.62 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.002 0.001 HIS H 38 PHE 0.023 0.001 PHE A 73 TYR 0.014 0.001 TYR A 625 ARG 0.003 0.000 ARG A 614 *********************** 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 164 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.7654 (ttm) cc_final: 0.7438 (ttm) REVERT: A 173 TYR cc_start: 0.7459 (m-80) cc_final: 0.7239 (m-80) REVERT: A 217 MET cc_start: 0.7913 (mmp) cc_final: 0.7580 (mmp) REVERT: A 253 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6727 (mtm110) REVERT: A 386 PHE cc_start: 0.8077 (t80) cc_final: 0.7399 (t80) REVERT: A 390 MET cc_start: 0.7178 (mtm) cc_final: 0.6837 (mtm) REVERT: A 417 MET cc_start: 0.6598 (mmm) cc_final: 0.6271 (mmm) REVERT: A 533 LYS cc_start: 0.7949 (mttm) cc_final: 0.7701 (mttm) REVERT: A 545 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7878 (mm) REVERT: A 601 LYS cc_start: 0.7548 (tttp) cc_final: 0.7195 (tttp) REVERT: A 631 MET cc_start: 0.6738 (tpp) cc_final: 0.6235 (tpp) REVERT: H 32 PHE cc_start: 0.8274 (t80) cc_final: 0.8040 (t80) REVERT: L 18 ASP cc_start: 0.6001 (m-30) cc_final: 0.5706 (m-30) REVERT: L 43 LYS cc_start: 0.7720 (mmtm) cc_final: 0.7511 (mmtm) outliers start: 35 outliers final: 18 residues processed: 153 average time/residue: 0.1572 time to fit residues: 32.3332 Evaluate side-chains 144 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5491 Z= 0.215 Angle : 0.603 7.421 7452 Z= 0.307 Chirality : 0.042 0.172 847 Planarity : 0.004 0.043 905 Dihedral : 7.323 58.356 877 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 6.20 % Allowed : 17.73 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.32), residues: 669 helix: 0.98 (0.31), residues: 296 sheet: -0.96 (0.60), residues: 83 loop : -2.48 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.015 0.001 PHE A 73 TYR 0.017 0.001 TYR L 50 ARG 0.004 0.000 ARG A 614 *********************** 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: 36 poor density : 135 time to evaluate : 0.594 Fit side-chains REVERT: A 58 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6250 (ttp80) REVERT: A 173 TYR cc_start: 0.7451 (m-80) cc_final: 0.7227 (m-80) REVERT: A 176 MET cc_start: 0.6725 (mmt) cc_final: 0.6514 (mmt) REVERT: A 217 MET cc_start: 0.7940 (mmp) cc_final: 0.7665 (mmp) REVERT: A 253 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7154 (mtm110) REVERT: A 386 PHE cc_start: 0.8035 (t80) cc_final: 0.7252 (t80) REVERT: A 390 MET cc_start: 0.7185 (mtm) cc_final: 0.6806 (mtm) REVERT: A 404 THR cc_start: 0.6213 (OUTLIER) cc_final: 0.5949 (m) REVERT: A 440 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6547 (ttp) REVERT: A 533 LYS cc_start: 0.7956 (mttm) cc_final: 0.7709 (mttm) REVERT: A 545 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7864 (mm) REVERT: A 601 LYS cc_start: 0.7503 (tttp) cc_final: 0.7140 (tttp) REVERT: A 631 MET cc_start: 0.6749 (tpp) cc_final: 0.6257 (tpp) REVERT: L 43 LYS cc_start: 0.7707 (mmtm) cc_final: 0.7496 (mmtm) outliers start: 36 outliers final: 26 residues processed: 156 average time/residue: 0.1586 time to fit residues: 32.5925 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 : 0.597 ------------------------------------------------------------------------------- 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 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 440 MET 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 637 LEU Chi-restraints excluded: chain H residue 20 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 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 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 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5491 Z= 0.209 Angle : 0.596 7.692 7452 Z= 0.301 Chirality : 0.041 0.162 847 Planarity : 0.004 0.043 905 Dihedral : 7.029 60.581 875 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 6.88 % Allowed : 19.45 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.32), residues: 669 helix: 1.22 (0.31), residues: 296 sheet: -0.88 (0.60), residues: 83 loop : -2.49 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.014 0.001 PHE A 73 TYR 0.016 0.001 TYR L 50 ARG 0.006 0.000 ARG A 614 *********************** 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 171 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.573 Fit side-chains REVERT: A 58 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6268 (ttp80) REVERT: A 173 TYR cc_start: 0.7409 (m-80) cc_final: 0.7184 (m-80) REVERT: A 176 MET cc_start: 0.6725 (mmt) cc_final: 0.6483 (mmt) REVERT: A 217 MET cc_start: 0.8003 (mmp) cc_final: 0.7793 (mmp) REVERT: A 253 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7118 (mtm110) REVERT: A 386 PHE cc_start: 0.7973 (t80) cc_final: 0.7256 (t80) REVERT: A 390 MET cc_start: 0.7184 (mtm) cc_final: 0.6817 (mtm) REVERT: A 404 THR cc_start: 0.6208 (OUTLIER) cc_final: 0.5950 (m) REVERT: A 440 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6566 (ttp) REVERT: A 463 CYS cc_start: 0.3854 (t) cc_final: 0.2838 (t) REVERT: A 533 LYS cc_start: 0.7955 (mttm) cc_final: 0.7717 (mttm) REVERT: A 545 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7848 (mm) REVERT: A 601 LYS cc_start: 0.7422 (tttp) cc_final: 0.7076 (tttp) REVERT: A 631 MET cc_start: 0.6763 (tpp) cc_final: 0.6251 (tpp) REVERT: H 93 ASP cc_start: 0.7180 (m-30) cc_final: 0.6891 (m-30) REVERT: L 43 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7446 (mmtm) REVERT: L 97 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6206 (mm) outliers start: 40 outliers final: 27 residues processed: 157 average time/residue: 0.1593 time to fit residues: 33.0665 Evaluate side-chains 162 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 440 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 594 LEU 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 99 CYS 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 103 THR 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 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 0.0980 chunk 58 optimal weight: 0.0010 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5491 Z= 0.166 Angle : 0.581 7.954 7452 Z= 0.289 Chirality : 0.040 0.133 847 Planarity : 0.004 0.043 905 Dihedral : 6.800 62.154 874 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 6.02 % Allowed : 20.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.32), residues: 669 helix: 1.43 (0.31), residues: 296 sheet: -0.76 (0.59), residues: 83 loop : -2.40 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.027 0.001 PHE H 32 TYR 0.012 0.001 TYR L 50 ARG 0.006 0.000 ARG A 614 *********************** 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 164 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.528 Fit side-chains REVERT: A 58 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6234 (ttp80) REVERT: A 176 MET cc_start: 0.6736 (mmt) cc_final: 0.6463 (mmt) REVERT: A 217 MET cc_start: 0.7989 (mmp) cc_final: 0.7780 (mmp) REVERT: A 253 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7102 (mtm110) REVERT: A 386 PHE cc_start: 0.7900 (t80) cc_final: 0.7240 (t80) REVERT: A 390 MET cc_start: 0.7178 (mtm) cc_final: 0.6854 (mtm) REVERT: A 440 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6562 (ttp) REVERT: A 463 CYS cc_start: 0.3793 (t) cc_final: 0.2805 (t) REVERT: A 533 LYS cc_start: 0.7923 (mttm) cc_final: 0.7712 (mttm) REVERT: A 545 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7824 (mm) REVERT: A 601 LYS cc_start: 0.7309 (tttp) cc_final: 0.6997 (tttp) REVERT: A 631 MET cc_start: 0.6791 (tpp) cc_final: 0.6298 (tpp) REVERT: H 93 ASP cc_start: 0.7163 (m-30) cc_final: 0.6868 (m-30) REVERT: L 43 LYS cc_start: 0.7648 (mmtm) cc_final: 0.7403 (mmtm) REVERT: L 97 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6179 (mm) outliers start: 35 outliers final: 22 residues processed: 153 average time/residue: 0.1545 time to fit residues: 31.2869 Evaluate side-chains 153 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 521 LEU 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 A residue 637 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 62 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5491 Z= 0.174 Angle : 0.580 7.837 7452 Z= 0.288 Chirality : 0.041 0.160 847 Planarity : 0.004 0.042 905 Dihedral : 6.617 62.496 872 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 6.54 % Allowed : 19.79 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.33), residues: 669 helix: 1.46 (0.31), residues: 296 sheet: -0.64 (0.59), residues: 83 loop : -2.29 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.020 0.001 PHE H 32 TYR 0.014 0.001 TYR L 50 ARG 0.002 0.000 ARG A 614 *********************** 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 171 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6241 (ttp80) REVERT: A 173 TYR cc_start: 0.7340 (m-80) cc_final: 0.7131 (m-80) REVERT: A 176 MET cc_start: 0.6756 (mmt) cc_final: 0.6449 (mmt) REVERT: A 217 MET cc_start: 0.8014 (mmp) cc_final: 0.7804 (mmp) REVERT: A 253 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7054 (mtm110) REVERT: A 386 PHE cc_start: 0.7892 (t80) cc_final: 0.7236 (t80) REVERT: A 390 MET cc_start: 0.7186 (mtm) cc_final: 0.6873 (mtm) REVERT: A 440 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6631 (ttp) REVERT: A 463 CYS cc_start: 0.3751 (t) cc_final: 0.2810 (t) REVERT: A 533 LYS cc_start: 0.7921 (mttm) cc_final: 0.7587 (mttm) REVERT: A 545 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7794 (mm) REVERT: A 601 LYS cc_start: 0.7303 (tttp) cc_final: 0.6989 (tttp) REVERT: A 631 MET cc_start: 0.6797 (tpp) cc_final: 0.6294 (tpp) REVERT: H 93 ASP cc_start: 0.7156 (m-30) cc_final: 0.6852 (m-30) REVERT: L 43 LYS cc_start: 0.7633 (mmtm) cc_final: 0.7419 (mmtm) REVERT: L 97 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6229 (mm) outliers start: 38 outliers final: 28 residues processed: 155 average time/residue: 0.1558 time to fit residues: 31.8842 Evaluate side-chains 165 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 123 TYR 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 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 440 MET 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 594 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 37 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 67 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.003 0.027 5491 Z= 0.197 Angle : 0.600 7.264 7452 Z= 0.299 Chirality : 0.041 0.149 847 Planarity : 0.004 0.043 905 Dihedral : 6.647 62.465 871 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 6.88 % Allowed : 19.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.33), residues: 669 helix: 1.48 (0.31), residues: 296 sheet: -0.78 (0.60), residues: 83 loop : -2.30 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.022 0.001 PHE H 32 TYR 0.015 0.001 TYR L 50 ARG 0.007 0.000 ARG A 614 *********************** 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 176 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6263 (ttp80) REVERT: A 173 TYR cc_start: 0.7335 (m-80) cc_final: 0.7120 (m-80) REVERT: A 176 MET cc_start: 0.6748 (mmt) cc_final: 0.6454 (mmt) REVERT: A 217 MET cc_start: 0.8024 (mmp) cc_final: 0.7802 (mmp) REVERT: A 253 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7034 (mtm110) REVERT: A 386 PHE cc_start: 0.7904 (t80) cc_final: 0.7246 (t80) REVERT: A 390 MET cc_start: 0.7175 (mtm) cc_final: 0.6862 (mtm) REVERT: A 440 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6628 (ttp) REVERT: A 463 CYS cc_start: 0.3829 (t) cc_final: 0.2869 (t) REVERT: A 533 LYS cc_start: 0.7996 (mttm) cc_final: 0.7665 (mttm) REVERT: A 545 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7800 (mm) REVERT: A 601 LYS cc_start: 0.7325 (tttp) cc_final: 0.7015 (tttp) REVERT: A 631 MET cc_start: 0.6786 (tpp) cc_final: 0.6295 (tpp) REVERT: H 93 ASP cc_start: 0.7146 (m-30) cc_final: 0.6850 (m-30) REVERT: L 43 LYS cc_start: 0.7653 (mmtm) cc_final: 0.7417 (mmtm) REVERT: L 97 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6242 (mm) outliers start: 40 outliers final: 32 residues processed: 159 average time/residue: 0.1576 time to fit residues: 33.0591 Evaluate side-chains 170 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 123 TYR 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 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 439 THR Chi-restraints excluded: chain A residue 440 MET 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 594 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 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 58 SER Chi-restraints excluded: chain H residue 67 VAL 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 92 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 50 optimal weight: 0.0030 chunk 58 optimal weight: 0.0470 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.4288 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5491 Z= 0.174 Angle : 0.602 8.515 7452 Z= 0.297 Chirality : 0.041 0.151 847 Planarity : 0.004 0.044 905 Dihedral : 6.538 62.923 871 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 6.37 % Allowed : 20.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.33), residues: 669 helix: 1.52 (0.31), residues: 296 sheet: -0.69 (0.61), residues: 83 loop : -2.25 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.023 0.001 PHE H 32 TYR 0.013 0.001 TYR L 50 ARG 0.005 0.000 ARG H 101 *********************** 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 169 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6269 (ttp80) REVERT: A 173 TYR cc_start: 0.7306 (m-80) cc_final: 0.7092 (m-80) REVERT: A 176 MET cc_start: 0.6742 (mmt) cc_final: 0.6448 (mmt) REVERT: A 253 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7050 (mtm110) REVERT: A 386 PHE cc_start: 0.7874 (t80) cc_final: 0.7218 (t80) REVERT: A 390 MET cc_start: 0.7165 (mtm) cc_final: 0.6844 (mtm) REVERT: A 440 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6660 (ttp) REVERT: A 463 CYS cc_start: 0.3753 (t) cc_final: 0.2841 (t) REVERT: A 533 LYS cc_start: 0.8011 (mttm) cc_final: 0.7716 (mttm) REVERT: A 545 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7784 (mm) REVERT: A 601 LYS cc_start: 0.7226 (tttp) cc_final: 0.6938 (tttp) REVERT: A 631 MET cc_start: 0.6779 (tpp) cc_final: 0.6284 (tpp) REVERT: H 42 GLN cc_start: 0.7640 (tt0) cc_final: 0.7340 (tt0) REVERT: H 93 ASP cc_start: 0.7130 (m-30) cc_final: 0.6857 (m-30) REVERT: L 43 LYS cc_start: 0.7637 (mmtm) cc_final: 0.7407 (mmtm) REVERT: L 97 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6252 (mm) outliers start: 37 outliers final: 29 residues processed: 154 average time/residue: 0.1598 time to fit residues: 32.4078 Evaluate side-chains 162 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU 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 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 439 THR Chi-restraints excluded: chain A residue 440 MET 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 594 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 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 58 SER Chi-restraints excluded: chain H residue 67 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.0040 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 61 optimal weight: 0.2980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5491 Z= 0.160 Angle : 0.592 7.667 7452 Z= 0.293 Chirality : 0.040 0.176 847 Planarity : 0.004 0.043 905 Dihedral : 6.441 63.046 871 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 5.16 % Allowed : 21.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.33), residues: 669 helix: 1.56 (0.32), residues: 291 sheet: -0.13 (0.62), residues: 76 loop : -2.16 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 PHE 0.023 0.001 PHE H 32 TYR 0.011 0.001 TYR L 50 ARG 0.003 0.000 ARG H 101 *********************** 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 159 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 TYR cc_start: 0.7109 (t80) cc_final: 0.6865 (t80) REVERT: A 176 MET cc_start: 0.6732 (mmt) cc_final: 0.6440 (mmt) REVERT: A 390 MET cc_start: 0.7148 (mtm) cc_final: 0.6821 (mtm) REVERT: A 440 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6677 (ttp) REVERT: A 463 CYS cc_start: 0.3722 (t) cc_final: 0.2768 (t) REVERT: A 533 LYS cc_start: 0.8019 (mttm) cc_final: 0.7748 (mttm) REVERT: A 545 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7768 (mm) REVERT: A 601 LYS cc_start: 0.7134 (tttp) cc_final: 0.6885 (tttp) REVERT: A 631 MET cc_start: 0.6802 (tpp) cc_final: 0.6310 (tpp) REVERT: H 42 GLN cc_start: 0.7630 (tt0) cc_final: 0.7324 (tt0) REVERT: L 43 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7387 (mmtm) REVERT: L 97 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6231 (mm) outliers start: 30 outliers final: 25 residues processed: 146 average time/residue: 0.1587 time to fit residues: 30.8090 Evaluate side-chains 154 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU 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 340 MET 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 440 MET 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 594 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 20 SER Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 67 VAL 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 92 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5491 Z= 0.193 Angle : 0.612 7.677 7452 Z= 0.305 Chirality : 0.042 0.267 847 Planarity : 0.004 0.043 905 Dihedral : 6.112 62.597 863 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.82 % Allowed : 22.38 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.33), residues: 669 helix: 1.55 (0.32), residues: 288 sheet: -0.34 (0.61), residues: 81 loop : -2.12 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.001 0.001 HIS A 115 PHE 0.024 0.001 PHE H 32 TYR 0.015 0.001 TYR L 50 ARG 0.004 0.000 ARG H 101 ********************** 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 157 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6274 (ttp80) REVERT: A 169 TYR cc_start: 0.7118 (t80) cc_final: 0.6860 (t80) REVERT: A 176 MET cc_start: 0.6750 (mmt) cc_final: 0.6461 (mmt) REVERT: A 386 PHE cc_start: 0.7876 (t80) cc_final: 0.7301 (t80) REVERT: A 390 MET cc_start: 0.7143 (mtm) cc_final: 0.6841 (mtm) REVERT: A 440 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6684 (ttp) REVERT: A 463 CYS cc_start: 0.3791 (t) cc_final: 0.2842 (t) REVERT: A 533 LYS cc_start: 0.8029 (mttm) cc_final: 0.7758 (mttm) REVERT: A 545 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7778 (mm) REVERT: A 601 LYS cc_start: 0.7247 (tttp) cc_final: 0.6971 (tttp) REVERT: A 631 MET cc_start: 0.6812 (tpp) cc_final: 0.6315 (tpp) REVERT: H 42 GLN cc_start: 0.7630 (tt0) cc_final: 0.7305 (tt0) REVERT: H 93 ASP cc_start: 0.7129 (m-30) cc_final: 0.6877 (m-30) REVERT: L 43 LYS cc_start: 0.7640 (mmtm) cc_final: 0.7396 (mmtm) REVERT: L 97 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6349 (mm) outliers start: 28 outliers final: 23 residues processed: 144 average time/residue: 0.1469 time to fit residues: 28.6298 Evaluate side-chains 156 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 340 MET 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 440 MET 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 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 58 SER Chi-restraints excluded: chain H residue 67 VAL 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 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.0000 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3913 r_free = 0.3913 target = 0.147391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128159 restraints weight = 8857.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131960 restraints weight = 4406.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134458 restraints weight = 2731.076| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5491 Z= 0.196 Angle : 0.610 7.638 7452 Z= 0.305 Chirality : 0.042 0.240 847 Planarity : 0.004 0.043 905 Dihedral : 6.127 62.691 863 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.99 % Allowed : 22.38 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.32), residues: 669 helix: 1.52 (0.31), residues: 288 sheet: -0.24 (0.61), residues: 81 loop : -2.11 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.024 0.001 PHE H 32 TYR 0.015 0.001 TYR L 50 ARG 0.004 0.000 ARG H 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.11 seconds wall clock time: 34 minutes 5.05 seconds (2045.05 seconds total)