Starting phenix.real_space_refine on Fri Apr 5 21:58:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/04_2024/8pg0_17655_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/04_2024/8pg0_17655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/04_2024/8pg0_17655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/04_2024/8pg0_17655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/04_2024/8pg0_17655_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/04_2024/8pg0_17655_updated.pdb" } resolution = 2.97 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= -0.000 sd= 0.001 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 38 5.16 5 C 3826 2.51 5 N 912 2.21 5 O 1040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A TYR 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: 5816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3986 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 511, 3978 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 17, 'TRANS': 493} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 511, 3978 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 17, 'TRANS': 493} Chain breaks: 8 bond proxies already assigned to first conformer: 4066 Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 758 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Unusual residues: {'BCT': 1, 'CLR': 3, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP A 70 " occ=0.58 ... (14 atoms not shown) pdb=" OD2BASP A 70 " occ=0.42 Time building chain proxies: 5.61, per 1000 atoms: 0.96 Number of scatterers: 5816 At special positions: 0 Unit cell: (78.03, 119.85, 104.04, 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 38 16.00 O 1040 8.00 N 912 7.00 C 3826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " 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=2.03 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 503 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 5 sheets defined 47.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 27 through 59 removed outlier: 3.839A pdb=" N ILE A 52 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLN A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 86 removed outlier: 4.048A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU A 74 " --> pdb=" O AASP A 70 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 117 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 170 through 199 removed outlier: 3.600A pdb=" N THR A 186 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Proline residue: A 187 - end of helix Proline residue: A 190 - end of helix removed outlier: 3.593A pdb=" N ASP A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 198 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 199 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 231 removed outlier: 3.921A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 258 through 276 Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 371 through 400 Proline residue: A 384 - end of helix removed outlier: 3.946A pdb=" N PHE A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 425 Processing helix chain 'A' and resid 458 through 461 No H-bonds generated for 'chain 'A' and resid 458 through 461' Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 528 through 560 removed outlier: 3.940A pdb=" N THR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 584 removed outlier: 3.586A pdb=" N LYS A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 580 " --> pdb=" O MET A 577 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 581 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 582 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 583 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 removed outlier: 3.613A pdb=" N LEU A 594 " --> pdb=" O TYR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 648 removed outlier: 4.060A pdb=" N SER A 629 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Proline residue: A 635 - end of helix Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= B, first strand: chain 'H' and resid 96 through 101 removed outlier: 3.638A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 103 through 105 removed outlier: 4.202A pdb=" N TYR H 103 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 63 through 67 removed outlier: 3.558A pdb=" N THR L 6 " --> pdb=" O ARG L 25 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN L 4 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 34 through 39 286 hydrogen bonds defined for protein. 754 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: 1.84 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.56: 5900 1.56 - 1.91: 59 1.91 - 2.25: 0 2.25 - 2.60: 0 2.60 - 2.95: 1 Bond restraints: 5960 Sorted by residual: bond pdb=" C TYR L 50 " pdb=" N SER L 53 " ideal model delta sigma weight residual 1.329 2.947 -1.618 1.40e-02 5.10e+03 1.34e+04 bond pdb=" C ARG A 526 " pdb=" N ASP A 527 " ideal model delta sigma weight residual 1.328 1.432 -0.104 1.44e-02 4.82e+03 5.20e+01 bond pdb=" C VAL A 221 " pdb=" N ILE A 222 " ideal model delta sigma weight residual 1.335 1.282 0.053 1.26e-02 6.30e+03 1.77e+01 bond pdb=" N VAL A 563 " pdb=" CA VAL A 563 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N GLY A 475 " pdb=" CA GLY A 475 " ideal model delta sigma weight residual 1.444 1.476 -0.031 1.06e-02 8.90e+03 8.83e+00 ... (remaining 5955 not shown) Histogram of bond angle deviations from ideal: 99.36 - 111.29: 2593 111.29 - 123.22: 5170 123.22 - 135.15: 314 135.15 - 147.08: 0 147.08 - 159.00: 1 Bond angle restraints: 8078 Sorted by residual: angle pdb=" C TYR L 50 " pdb=" N SER L 53 " pdb=" CA SER L 53 " ideal model delta sigma weight residual 121.70 159.00 -37.30 1.80e+00 3.09e-01 4.30e+02 angle pdb=" N ILE A 562 " pdb=" CA ILE A 562 " pdb=" C ILE A 562 " ideal model delta sigma weight residual 112.29 107.96 4.33 9.40e-01 1.13e+00 2.12e+01 angle pdb=" C SER L 10 " pdb=" CA SER L 10 " pdb=" CB SER L 10 " ideal model delta sigma weight residual 117.23 111.69 5.54 1.36e+00 5.41e-01 1.66e+01 angle pdb=" N ASN A 477 " pdb=" CA ASN A 477 " pdb=" C ASN A 477 " ideal model delta sigma weight residual 113.19 108.58 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N ASN A 476 " pdb=" CA ASN A 476 " pdb=" C ASN A 476 " ideal model delta sigma weight residual 112.87 108.30 4.57 1.20e+00 6.94e-01 1.45e+01 ... (remaining 8073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 3323 24.23 - 48.45: 246 48.45 - 72.68: 36 72.68 - 96.90: 5 96.90 - 121.13: 3 Dihedral angle restraints: 3613 sinusoidal: 1511 harmonic: 2102 Sorted by residual: dihedral pdb=" CA TYR L 50 " pdb=" C TYR L 50 " pdb=" N SER L 53 " pdb=" CA SER L 53 " ideal model delta harmonic sigma weight residual 0.00 -38.47 38.47 0 5.00e+00 4.00e-02 5.92e+01 dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 506 " pdb=" CB CYS A 506 " ideal model delta sinusoidal sigma weight residual 93.00 131.42 -38.42 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 524 " pdb=" CB CYS A 524 " ideal model delta sinusoidal sigma weight residual 93.00 55.20 37.80 1 1.00e+01 1.00e-02 2.01e+01 ... (remaining 3610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 795 0.083 - 0.166: 109 0.166 - 0.250: 19 0.250 - 0.333: 1 0.333 - 0.416: 1 Chirality restraints: 925 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 503 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C13 CLR A 805 " pdb=" C12 CLR A 805 " pdb=" C14 CLR A 805 " pdb=" C17 CLR A 805 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C14 CLR A 805 " pdb=" C13 CLR A 805 " pdb=" C15 CLR A 805 " pdb=" C8 CLR A 805 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 922 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 801 " 0.270 2.00e-02 2.50e+03 2.28e-01 6.47e+02 pdb=" C7 NAG A 801 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A 801 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG A 801 " -0.387 2.00e-02 2.50e+03 pdb=" O7 NAG A 801 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 50 " 0.023 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C TYR L 50 " -0.069 2.00e-02 2.50e+03 pdb=" O TYR L 50 " 0.032 2.00e-02 2.50e+03 pdb=" N SER L 53 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 471 " 0.053 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A 472 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 472 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 472 " 0.043 5.00e-02 4.00e+02 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 595 2.75 - 3.29: 6052 3.29 - 3.82: 9943 3.82 - 4.36: 12109 4.36 - 4.90: 20247 Nonbonded interactions: 48946 Sorted by model distance: nonbonded pdb=" OE1 GLN A 366 " pdb=" OG SER A 618 " model vdw 2.211 2.440 nonbonded pdb=" O PRO A 472 " pdb=" O LEU A 521 " model vdw 2.252 3.040 nonbonded pdb=" O SER H 33 " pdb=" OG SER H 57 " model vdw 2.280 2.440 nonbonded pdb=" O SER A 228 " pdb=" OG SER A 372 " model vdw 2.281 2.440 nonbonded pdb=" ND1 HIS A 115 " pdb=" O2 BCT A 802 " model vdw 2.299 2.520 ... (remaining 48941 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.700 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: 22.360 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.570 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.022 1.618 5960 Z= 1.844 Angle : 0.943 37.304 8078 Z= 0.587 Chirality : 0.058 0.416 925 Planarity : 0.009 0.228 969 Dihedral : 16.430 121.126 2251 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 0.80 % Allowed : 24.12 % Favored : 75.08 % 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: 0.35 (0.32), residues: 714 helix: 1.26 (0.28), residues: 348 sheet: -0.12 (0.54), residues: 105 loop : -0.98 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS A 451 PHE 0.011 0.001 PHE A 175 TYR 0.018 0.001 TYR A 590 ARG 0.003 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.618 Fit side-chains REVERT: A 640 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6864 (t80) REVERT: H 21 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7055 (tp) outliers start: 5 outliers final: 1 residues processed: 107 average time/residue: 0.8365 time to fit residues: 95.5801 Evaluate side-chains 91 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN A 476 ASN L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5960 Z= 0.240 Angle : 0.655 9.010 8078 Z= 0.323 Chirality : 0.044 0.223 925 Planarity : 0.005 0.047 969 Dihedral : 7.965 82.562 1009 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.37 % Favored : 96.49 % Rotamer: Outliers : 5.11 % Allowed : 22.04 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.52 (0.32), residues: 716 helix: 1.39 (0.28), residues: 352 sheet: 0.06 (0.53), residues: 108 loop : -0.96 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 254 HIS 0.002 0.001 HIS A 169 PHE 0.011 0.001 PHE A 643 TYR 0.014 0.001 TYR A 590 ARG 0.004 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 0.668 Fit side-chains REVERT: A 390 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5827 (ptm) REVERT: A 446 ASN cc_start: 0.6139 (m-40) cc_final: 0.5920 (m-40) REVERT: A 640 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7464 (t80) REVERT: H 21 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7232 (tp) REVERT: L 67 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5819 (ppt170) outliers start: 32 outliers final: 13 residues processed: 118 average time/residue: 0.7237 time to fit residues: 92.3988 Evaluate side-chains 104 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5960 Z= 0.172 Angle : 0.608 12.011 8078 Z= 0.294 Chirality : 0.042 0.212 925 Planarity : 0.004 0.043 969 Dihedral : 7.218 80.308 1007 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.15 % Allowed : 24.28 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.67 (0.33), residues: 716 helix: 1.42 (0.28), residues: 352 sheet: 0.18 (0.54), residues: 105 loop : -0.74 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.002 0.001 HIS A 451 PHE 0.011 0.001 PHE A 547 TYR 0.018 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.620 Fit side-chains REVERT: A 446 ASN cc_start: 0.6243 (m-40) cc_final: 0.6026 (m-40) REVERT: A 640 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7453 (t80) REVERT: H 21 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7029 (tp) REVERT: L 48 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7129 (mt) REVERT: L 67 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.5937 (ppt170) outliers start: 26 outliers final: 10 residues processed: 109 average time/residue: 0.7775 time to fit residues: 91.1844 Evaluate side-chains 103 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5960 Z= 0.163 Angle : 0.589 8.875 8078 Z= 0.286 Chirality : 0.041 0.215 925 Planarity : 0.004 0.043 969 Dihedral : 6.872 69.932 1007 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.35 % Allowed : 26.04 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 716 helix: 1.42 (0.28), residues: 350 sheet: 0.42 (0.55), residues: 103 loop : -0.74 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.002 0.001 HIS A 451 PHE 0.009 0.001 PHE A 360 TYR 0.018 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.647 Fit side-chains REVERT: A 199 PHE cc_start: 0.6631 (m-10) cc_final: 0.6421 (m-10) REVERT: A 239 TYR cc_start: 0.6959 (m-10) cc_final: 0.6056 (m-10) REVERT: A 446 ASN cc_start: 0.6326 (m-40) cc_final: 0.6023 (m110) REVERT: A 596 ASP cc_start: 0.7939 (m-30) cc_final: 0.7711 (m-30) REVERT: A 640 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7451 (t80) REVERT: H 21 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7016 (tp) REVERT: L 48 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7166 (mt) REVERT: L 67 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5858 (ppt170) outliers start: 21 outliers final: 10 residues processed: 110 average time/residue: 0.7877 time to fit residues: 92.9356 Evaluate side-chains 111 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5960 Z= 0.324 Angle : 0.703 9.068 8078 Z= 0.348 Chirality : 0.045 0.238 925 Planarity : 0.005 0.047 969 Dihedral : 7.584 61.920 1007 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.31 % Allowed : 25.40 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.30 (0.32), residues: 716 helix: 0.92 (0.28), residues: 349 sheet: 0.79 (0.56), residues: 92 loop : -0.90 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 36 HIS 0.003 0.001 HIS A 520 PHE 0.017 0.002 PHE A 73 TYR 0.012 0.002 TYR H 83 ARG 0.004 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.641 Fit side-chains REVERT: A 390 MET cc_start: 0.6067 (pp-130) cc_final: 0.5695 (ptm) REVERT: A 446 ASN cc_start: 0.6611 (m-40) cc_final: 0.6304 (m110) REVERT: A 640 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7446 (t80) REVERT: H 21 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7010 (tp) REVERT: H 114 ASP cc_start: 0.7881 (t0) cc_final: 0.6833 (t0) REVERT: H 117 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6621 (mpt) REVERT: L 48 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7388 (mt) REVERT: L 67 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.5933 (ppt170) outliers start: 27 outliers final: 15 residues processed: 115 average time/residue: 0.8128 time to fit residues: 99.8695 Evaluate side-chains 111 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.0040 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 544 ASN H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5960 Z= 0.235 Angle : 0.640 8.496 8078 Z= 0.316 Chirality : 0.043 0.228 925 Planarity : 0.004 0.046 969 Dihedral : 7.011 58.096 1007 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.47 % Allowed : 25.88 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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 (0.32), residues: 716 helix: 1.00 (0.28), residues: 349 sheet: 0.86 (0.56), residues: 92 loop : -0.90 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.003 0.001 HIS A 169 PHE 0.013 0.001 PHE A 643 TYR 0.016 0.001 TYR A 590 ARG 0.003 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.643 Fit side-chains REVERT: A 83 PHE cc_start: 0.7121 (m-10) cc_final: 0.6748 (m-80) REVERT: A 446 ASN cc_start: 0.6606 (m-40) cc_final: 0.6343 (m110) REVERT: A 640 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7369 (t80) REVERT: H 21 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6985 (tp) REVERT: H 117 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6679 (mpt) REVERT: L 67 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5904 (ppt170) REVERT: L 91 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6280 (tt0) outliers start: 28 outliers final: 16 residues processed: 112 average time/residue: 0.7957 time to fit residues: 95.4105 Evaluate side-chains 112 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.0670 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 422 GLN H 80 ASN L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5960 Z= 0.162 Angle : 0.594 9.542 8078 Z= 0.289 Chirality : 0.041 0.214 925 Planarity : 0.004 0.044 969 Dihedral : 6.272 58.793 1007 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.67 % Allowed : 27.48 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.59 (0.32), residues: 716 helix: 1.26 (0.28), residues: 350 sheet: 0.43 (0.54), residues: 102 loop : -0.72 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 169 PHE 0.011 0.001 PHE A 547 TYR 0.019 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6968 (m-10) cc_final: 0.6669 (m-80) REVERT: A 390 MET cc_start: 0.6056 (pp-130) cc_final: 0.5683 (ptm) REVERT: A 446 ASN cc_start: 0.6444 (m-40) cc_final: 0.6197 (m110) REVERT: A 640 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7456 (t80) REVERT: H 21 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6946 (tp) REVERT: L 48 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7255 (mt) REVERT: L 67 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5818 (ppt170) outliers start: 23 outliers final: 12 residues processed: 112 average time/residue: 0.8458 time to fit residues: 101.4414 Evaluate side-chains 112 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 0.0060 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5960 Z= 0.172 Angle : 0.592 8.542 8078 Z= 0.291 Chirality : 0.041 0.218 925 Planarity : 0.004 0.044 969 Dihedral : 6.062 59.292 1007 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.99 % Allowed : 27.96 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.67 (0.32), residues: 716 helix: 1.31 (0.28), residues: 350 sheet: 0.47 (0.54), residues: 102 loop : -0.66 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.003 0.001 HIS A 169 PHE 0.011 0.001 PHE A 643 TYR 0.017 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6962 (m-10) cc_final: 0.6685 (m-80) REVERT: A 446 ASN cc_start: 0.6424 (m-40) cc_final: 0.6179 (m110) REVERT: A 640 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 650 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8020 (mptm) REVERT: H 21 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6940 (tp) REVERT: L 48 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7279 (mt) REVERT: L 67 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5709 (ppt170) outliers start: 25 outliers final: 15 residues processed: 122 average time/residue: 0.8006 time to fit residues: 104.4642 Evaluate side-chains 118 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5960 Z= 0.203 Angle : 0.619 8.798 8078 Z= 0.306 Chirality : 0.042 0.222 925 Planarity : 0.004 0.045 969 Dihedral : 6.130 59.242 1007 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.99 % Allowed : 28.43 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.57 (0.32), residues: 716 helix: 1.24 (0.28), residues: 349 sheet: 0.44 (0.54), residues: 102 loop : -0.75 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.003 0.001 HIS A 169 PHE 0.010 0.001 PHE A 643 TYR 0.016 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.589 Fit side-chains REVERT: A 390 MET cc_start: 0.6005 (pp-130) cc_final: 0.5627 (ptm) REVERT: A 446 ASN cc_start: 0.6529 (m-40) cc_final: 0.6286 (m110) REVERT: A 640 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7393 (t80) REVERT: A 650 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8020 (mptm) REVERT: H 21 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6955 (tp) REVERT: L 48 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7296 (mt) outliers start: 25 outliers final: 16 residues processed: 115 average time/residue: 0.8572 time to fit residues: 105.7972 Evaluate side-chains 116 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5960 Z= 0.192 Angle : 0.608 8.494 8078 Z= 0.301 Chirality : 0.042 0.220 925 Planarity : 0.004 0.045 969 Dihedral : 6.023 58.876 1007 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.51 % Allowed : 29.07 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.55 (0.32), residues: 716 helix: 1.24 (0.28), residues: 349 sheet: 0.39 (0.53), residues: 102 loop : -0.78 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.004 0.001 HIS A 169 PHE 0.012 0.001 PHE A 643 TYR 0.016 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7129 (m-10) cc_final: 0.6753 (m-80) REVERT: A 390 MET cc_start: 0.6007 (pp-130) cc_final: 0.5512 (ptm) REVERT: A 446 ASN cc_start: 0.6537 (m-40) cc_final: 0.6286 (m110) REVERT: A 640 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7428 (t80) REVERT: A 650 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8040 (mptm) REVERT: H 21 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6954 (tp) REVERT: L 48 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7293 (mt) REVERT: L 67 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5868 (ppt170) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.8118 time to fit residues: 99.3165 Evaluate side-chains 117 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138800 restraints weight = 19975.035| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.76 r_work: 0.3561 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5960 Z= 0.170 Angle : 0.588 8.484 8078 Z= 0.291 Chirality : 0.041 0.217 925 Planarity : 0.004 0.045 969 Dihedral : 5.809 57.339 1007 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.67 % Allowed : 29.23 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.62 (0.32), residues: 716 helix: 1.32 (0.28), residues: 349 sheet: 0.40 (0.54), residues: 102 loop : -0.76 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.003 0.001 HIS A 169 PHE 0.013 0.001 PHE A 83 TYR 0.018 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2650.86 seconds wall clock time: 48 minutes 21.72 seconds (2901.72 seconds total)