Starting phenix.real_space_refine on Fri Apr 5 20:31:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/04_2024/8phw_17677.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/04_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_17677/04_2024/8phw_17677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/04_2024/8phw_17677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/04_2024/8phw_17677.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phw_17677/04_2024/8phw_17677.pdb" } 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 Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.55, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 943.7 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: 0.54 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: 1.47 Time building geometry restraints manager: 2.18 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: 99.45 - 106.37: 135 106.37 - 113.29: 2974 113.29 - 120.20: 1959 120.20 - 127.12: 2330 127.12 - 134.04: 54 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 2.440 nonbonded pdb=" O ALA A 415 " pdb=" OG SER A 418 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.235 2.440 nonbonded pdb=" NH2 ARG H 70 " pdb=" O SER H 88 " model vdw 2.248 2.520 nonbonded pdb=" O CYS A 474 " pdb=" N ALA A 519 " model vdw 2.252 2.520 ... (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 ========== 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: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 21.620 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.970 Find NCS groups from input model: 0.140 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.180 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 0.533 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: 0.1551 time to fit residues: 34.4081 Evaluate side-chains 147 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 0.0570 chunk 50 optimal weight: 0.0000 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 0.4102 ------------------------------------------------------------------------------- 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: 0.6961 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5491 Z= 0.168 Angle : 0.580 7.455 7452 Z= 0.298 Chirality : 0.041 0.257 847 Planarity : 0.005 0.058 905 Dihedral : 8.084 59.111 886 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 7.06 % Allowed : 13.94 % 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 (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: -1.62 (0.30), residues: 669 helix: 0.27 (0.29), residues: 291 sheet: -0.80 (0.60), residues: 75 loop : -2.57 (0.30), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 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 0.004 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 171 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 217 MET cc_start: 0.7919 (mmp) cc_final: 0.7566 (mmp) REVERT: A 253 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6719 (mtm110) REVERT: A 386 PHE cc_start: 0.8099 (t80) cc_final: 0.7363 (t80) REVERT: A 390 MET cc_start: 0.7190 (mtm) cc_final: 0.6820 (mtm) REVERT: A 404 THR cc_start: 0.6194 (OUTLIER) cc_final: 0.5906 (m) REVERT: A 533 LYS cc_start: 0.7946 (mttm) cc_final: 0.7698 (mttm) REVERT: A 545 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7874 (mm) REVERT: A 601 LYS cc_start: 0.7523 (tttp) cc_final: 0.7183 (tttp) REVERT: A 631 MET cc_start: 0.6746 (tpp) cc_final: 0.6226 (tpp) REVERT: H 32 PHE cc_start: 0.8261 (t80) cc_final: 0.8017 (t80) outliers start: 41 outliers final: 22 residues processed: 156 average time/residue: 0.1484 time to fit residues: 31.1025 Evaluate side-chains 151 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET 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 225 THR 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 404 THR 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 A residue 605 ASN 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 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.0020 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5491 Z= 0.222 Angle : 0.598 7.394 7452 Z= 0.305 Chirality : 0.041 0.164 847 Planarity : 0.004 0.045 905 Dihedral : 7.217 58.117 877 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 6.88 % Allowed : 18.42 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.32), residues: 669 helix: 0.93 (0.30), residues: 296 sheet: -1.04 (0.59), residues: 83 loop : -2.44 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 254 HIS 0.002 0.001 HIS H 38 PHE 0.015 0.001 PHE A 73 TYR 0.018 0.002 TYR L 50 ARG 0.006 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 169 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6246 (ttp80) REVERT: A 173 TYR cc_start: 0.7468 (m-80) cc_final: 0.7243 (m-80) REVERT: A 176 MET cc_start: 0.6729 (mmt) cc_final: 0.6521 (mmt) REVERT: A 217 MET cc_start: 0.7949 (mmp) cc_final: 0.7668 (mmp) REVERT: A 253 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7066 (mtm110) REVERT: A 386 PHE cc_start: 0.8087 (t80) cc_final: 0.7334 (t80) REVERT: A 390 MET cc_start: 0.7206 (mtm) cc_final: 0.6819 (mtm) REVERT: A 440 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6593 (ttp) REVERT: A 533 LYS cc_start: 0.7959 (mttm) cc_final: 0.7706 (mttm) REVERT: A 545 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7856 (mm) REVERT: A 601 LYS cc_start: 0.7546 (tttp) cc_final: 0.7183 (tttp) REVERT: A 631 MET cc_start: 0.6764 (tpp) cc_final: 0.6247 (tpp) outliers start: 40 outliers final: 31 residues processed: 151 average time/residue: 0.1496 time to fit residues: 30.0357 Evaluate side-chains 162 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET 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 225 THR 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 261 ASN 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 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 605 ASN 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 58 SER Chi-restraints excluded: chain H residue 88 SER 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 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: 0.6980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5491 Z= 0.245 Angle : 0.603 7.851 7452 Z= 0.308 Chirality : 0.041 0.149 847 Planarity : 0.004 0.046 905 Dihedral : 7.143 60.424 874 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 8.09 % Allowed : 18.76 % 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: -0.90 (0.32), residues: 669 helix: 1.09 (0.30), residues: 297 sheet: -0.39 (0.64), residues: 74 loop : -2.53 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.032 0.001 PHE H 32 TYR 0.018 0.002 TYR L 50 ARG 0.007 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 175 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 128 time to evaluate : 0.560 Fit side-chains REVERT: A 58 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6270 (ttp80) REVERT: A 173 TYR cc_start: 0.7433 (m-80) cc_final: 0.7205 (m-80) REVERT: A 176 MET cc_start: 0.6734 (mmt) cc_final: 0.6491 (mmt) REVERT: A 217 MET cc_start: 0.8006 (mmp) cc_final: 0.7691 (mmp) REVERT: A 253 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6949 (mtm110) REVERT: A 386 PHE cc_start: 0.8053 (t80) cc_final: 0.7318 (t80) REVERT: A 390 MET cc_start: 0.7218 (mtm) cc_final: 0.6838 (mtm) REVERT: A 404 THR cc_start: 0.6261 (OUTLIER) cc_final: 0.5975 (m) REVERT: A 440 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6586 (ttp) REVERT: A 463 CYS cc_start: 0.4186 (t) cc_final: 0.3113 (t) REVERT: A 533 LYS cc_start: 0.7957 (mttm) cc_final: 0.7714 (mttm) REVERT: A 545 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7863 (mm) REVERT: A 601 LYS cc_start: 0.7534 (tttp) cc_final: 0.7169 (tttp) REVERT: A 631 MET cc_start: 0.6772 (tpp) cc_final: 0.6255 (tpp) REVERT: H 121 TYR cc_start: 0.7116 (m-80) cc_final: 0.6892 (m-80) REVERT: L 97 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6307 (mm) outliers start: 47 outliers final: 34 residues processed: 154 average time/residue: 0.1535 time to fit residues: 31.7035 Evaluate side-chains 167 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET 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 225 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 ASN 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 460 ASN 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 557 MET Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 ASN 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 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 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: 0.9980 chunk 26 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN A 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5491 Z= 0.201 Angle : 0.584 7.512 7452 Z= 0.294 Chirality : 0.040 0.139 847 Planarity : 0.004 0.047 905 Dihedral : 7.022 62.059 874 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 8.61 % Allowed : 18.07 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.32), residues: 669 helix: 1.34 (0.31), residues: 296 sheet: -0.47 (0.63), residues: 78 loop : -2.50 (0.31), residues: 295 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 0.018 0.001 PHE H 32 TYR 0.015 0.001 TYR L 50 ARG 0.005 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 179 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 129 time to evaluate : 0.590 Fit side-chains REVERT: A 58 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6282 (ttp80) REVERT: A 173 TYR cc_start: 0.7384 (m-80) cc_final: 0.7158 (m-80) REVERT: A 176 MET cc_start: 0.6745 (mmt) cc_final: 0.6474 (mmt) REVERT: A 217 MET cc_start: 0.7998 (mmp) cc_final: 0.7775 (mmp) REVERT: A 253 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6970 (mtm110) REVERT: A 386 PHE cc_start: 0.8014 (t80) cc_final: 0.7266 (t80) REVERT: A 390 MET cc_start: 0.7216 (mtm) cc_final: 0.6825 (mtm) REVERT: A 440 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6570 (ttp) REVERT: A 463 CYS cc_start: 0.4188 (t) cc_final: 0.3133 (t) REVERT: A 533 LYS cc_start: 0.7950 (mttm) cc_final: 0.7722 (mttm) REVERT: A 545 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7859 (mm) REVERT: A 601 LYS cc_start: 0.7424 (tttp) cc_final: 0.7083 (tttp) REVERT: A 631 MET cc_start: 0.6797 (tpp) cc_final: 0.6297 (tpp) REVERT: H 121 TYR cc_start: 0.7115 (m-80) cc_final: 0.6905 (m-80) REVERT: L 97 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6222 (mm) outliers start: 50 outliers final: 35 residues processed: 159 average time/residue: 0.1500 time to fit residues: 31.8799 Evaluate side-chains 167 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 MET 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 225 THR 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 261 ASN 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 460 ASN 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 576 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 ASN 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 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 15 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 34 optimal weight: 0.0060 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 36 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5491 Z= 0.153 Angle : 0.576 8.329 7452 Z= 0.281 Chirality : 0.040 0.136 847 Planarity : 0.004 0.045 905 Dihedral : 6.719 63.363 874 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 6.37 % Allowed : 19.62 % 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 (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: -0.47 (0.33), residues: 669 helix: 1.55 (0.31), residues: 296 sheet: -0.38 (0.62), residues: 78 loop : -2.37 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 115 PHE 0.017 0.001 PHE A 276 TYR 0.011 0.001 TYR A 239 ARG 0.001 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 162 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.6725 (mmt) cc_final: 0.6449 (mmt) REVERT: A 217 MET cc_start: 0.7997 (mmp) cc_final: 0.7785 (mmp) REVERT: A 386 PHE cc_start: 0.7933 (t80) cc_final: 0.7269 (t80) REVERT: A 390 MET cc_start: 0.7218 (mtm) cc_final: 0.6850 (mtm) REVERT: A 440 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6457 (ttp) REVERT: A 463 CYS cc_start: 0.3974 (t) cc_final: 0.2897 (t) REVERT: A 533 LYS cc_start: 0.7905 (mttm) cc_final: 0.7702 (mttm) REVERT: A 545 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7783 (mm) REVERT: A 601 LYS cc_start: 0.7227 (tttp) cc_final: 0.6935 (tttp) REVERT: A 631 MET cc_start: 0.6784 (tpp) cc_final: 0.6285 (tpp) REVERT: L 97 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6199 (mm) outliers start: 37 outliers final: 28 residues processed: 146 average time/residue: 0.1558 time to fit residues: 30.4468 Evaluate side-chains 152 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET 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 225 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 440 MET 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 575 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 ASN 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 15 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.0570 chunk 41 optimal weight: 0.9990 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN H 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2273 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= 0.211 Angle : 0.596 7.365 7452 Z= 0.296 Chirality : 0.041 0.142 847 Planarity : 0.004 0.046 905 Dihedral : 6.382 62.711 865 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 7.23 % Allowed : 19.45 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.33), residues: 669 helix: 1.49 (0.31), residues: 296 sheet: -0.39 (0.63), residues: 78 loop : -2.33 (0.32), residues: 295 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 0.012 0.001 PHE A 537 TYR 0.018 0.001 TYR L 50 ARG 0.008 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 174 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 0.627 Fit side-chains REVERT: A 58 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6249 (ttp80) REVERT: A 173 TYR cc_start: 0.7347 (m-80) cc_final: 0.7128 (m-80) REVERT: A 176 MET cc_start: 0.6743 (mmt) cc_final: 0.6467 (mmt) REVERT: A 386 PHE cc_start: 0.7957 (t80) cc_final: 0.7270 (t80) REVERT: A 390 MET cc_start: 0.7217 (mtm) cc_final: 0.6859 (mtm) REVERT: A 440 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6535 (ttp) REVERT: A 463 CYS cc_start: 0.4112 (t) cc_final: 0.3013 (t) REVERT: A 533 LYS cc_start: 0.7933 (mttm) cc_final: 0.7602 (mttm) REVERT: A 545 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7800 (mm) REVERT: A 601 LYS cc_start: 0.7352 (tttp) cc_final: 0.7024 (tttp) REVERT: A 631 MET cc_start: 0.6804 (tpp) cc_final: 0.6278 (tpp) REVERT: L 97 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6318 (mm) outliers start: 42 outliers final: 36 residues processed: 158 average time/residue: 0.1406 time to fit residues: 30.1966 Evaluate side-chains 173 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 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 29 MET 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 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 ASN 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 460 ASN 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 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 ASN 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 Chi-restraints excluded: chain L residue 103 THR 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: 1.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 0.0370 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2501 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 : 0.589 8.941 7452 Z= 0.289 Chirality : 0.040 0.147 847 Planarity : 0.004 0.046 905 Dihedral : 6.214 63.314 865 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 6.71 % Allowed : 20.48 % 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: -0.39 (0.33), residues: 669 helix: 1.60 (0.31), residues: 296 sheet: -0.38 (0.62), residues: 78 loop : -2.30 (0.33), residues: 295 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 0.017 0.001 PHE A 276 TYR 0.012 0.001 TYR L 50 ARG 0.006 0.000 ARG A 614 *********************** 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 167 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 169 TYR cc_start: 0.7122 (t80) cc_final: 0.6865 (t80) REVERT: A 176 MET cc_start: 0.6738 (mmt) cc_final: 0.6452 (mmt) REVERT: A 386 PHE cc_start: 0.7930 (t80) cc_final: 0.7252 (t80) REVERT: A 390 MET cc_start: 0.7180 (mtm) cc_final: 0.6835 (mtm) REVERT: A 440 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6528 (ttp) REVERT: A 463 CYS cc_start: 0.4016 (t) cc_final: 0.2961 (t) REVERT: A 533 LYS cc_start: 0.7995 (mttm) cc_final: 0.7676 (mttm) REVERT: A 545 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7773 (mm) REVERT: A 601 LYS cc_start: 0.7206 (tttp) cc_final: 0.6921 (tttp) REVERT: A 631 MET cc_start: 0.6811 (tpp) cc_final: 0.6305 (tpp) REVERT: H 42 GLN cc_start: 0.7640 (tt0) cc_final: 0.7341 (tt0) REVERT: L 97 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6218 (mm) outliers start: 39 outliers final: 34 residues processed: 152 average time/residue: 0.1513 time to fit residues: 31.2138 Evaluate side-chains 162 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 MET 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 225 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 ASN 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 460 ASN 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 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 ASN 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 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 15 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2561 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= 0.180 Angle : 0.595 8.325 7452 Z= 0.294 Chirality : 0.040 0.138 847 Planarity : 0.004 0.046 905 Dihedral : 6.214 63.244 865 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 6.88 % Allowed : 21.00 % Favored : 72.12 % 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 (0.33), residues: 669 helix: 1.58 (0.31), residues: 296 sheet: -0.24 (0.64), residues: 76 loop : -2.25 (0.32), residues: 297 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 0.009 0.001 PHE A 537 TYR 0.014 0.001 TYR L 50 ARG 0.001 0.000 ARG H 70 *********************** 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 169 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.654 Fit side-chains REVERT: A 58 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6238 (ttp80) REVERT: A 169 TYR cc_start: 0.7129 (t80) cc_final: 0.6876 (t80) REVERT: A 386 PHE cc_start: 0.7925 (t80) cc_final: 0.7244 (t80) REVERT: A 390 MET cc_start: 0.7187 (mtm) cc_final: 0.6839 (mtm) REVERT: A 440 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6545 (ttp) REVERT: A 463 CYS cc_start: 0.4011 (t) cc_final: 0.2932 (t) REVERT: A 533 LYS cc_start: 0.8012 (mttm) cc_final: 0.7733 (mttm) REVERT: A 545 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7778 (mm) REVERT: A 601 LYS cc_start: 0.7229 (tttp) cc_final: 0.6926 (tttp) REVERT: A 631 MET cc_start: 0.6811 (tpp) cc_final: 0.6303 (tpp) REVERT: L 97 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6286 (mm) outliers start: 40 outliers final: 35 residues processed: 151 average time/residue: 0.1483 time to fit residues: 30.5446 Evaluate side-chains 168 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 MET 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 199 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 ASN 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 460 ASN 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 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 ASN 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 15 SER Chi-restraints excluded: chain L residue 57 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5491 Z= 0.148 Angle : 0.581 7.873 7452 Z= 0.288 Chirality : 0.039 0.142 847 Planarity : 0.004 0.045 905 Dihedral : 6.097 63.740 865 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 6.37 % Allowed : 21.34 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.33), residues: 669 helix: 1.69 (0.31), residues: 296 sheet: -0.31 (0.63), residues: 78 loop : -2.09 (0.33), residues: 295 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 0.008 0.001 PHE A 73 TYR 0.010 0.001 TYR A 625 ARG 0.007 0.000 ARG A 614 ********************** 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 162 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8312 (tp) cc_final: 0.8111 (tp) REVERT: A 386 PHE cc_start: 0.7868 (t80) cc_final: 0.7214 (t80) REVERT: A 390 MET cc_start: 0.7170 (mtm) cc_final: 0.6845 (mtm) REVERT: A 440 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6564 (ttp) REVERT: A 533 LYS cc_start: 0.8003 (mttm) cc_final: 0.7736 (mttm) REVERT: A 545 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7732 (mm) REVERT: A 601 LYS cc_start: 0.7069 (tttp) cc_final: 0.6795 (tttp) REVERT: A 631 MET cc_start: 0.6792 (tpp) cc_final: 0.6293 (tpp) REVERT: L 97 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6259 (mm) outliers start: 37 outliers final: 31 residues processed: 146 average time/residue: 0.1505 time to fit residues: 29.6028 Evaluate side-chains 157 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 MET 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 244 THR Chi-restraints excluded: chain A residue 261 ASN 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 440 MET 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 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 ASN 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 15 SER Chi-restraints excluded: chain L residue 57 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.0020 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126976 restraints weight = 9000.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130782 restraints weight = 4506.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133262 restraints weight = 2815.893| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2751 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= 0.183 Angle : 0.590 7.631 7452 Z= 0.294 Chirality : 0.040 0.143 847 Planarity : 0.004 0.044 905 Dihedral : 6.072 63.194 863 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.02 % Allowed : 21.86 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.33), residues: 669 helix: 1.59 (0.31), residues: 297 sheet: -0.23 (0.63), residues: 78 loop : -2.07 (0.33), residues: 294 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 0.010 0.001 PHE A 73 TYR 0.015 0.001 TYR L 50 ARG 0.008 0.000 ARG A 614 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1877.22 seconds wall clock time: 34 minutes 48.22 seconds (2088.22 seconds total)