Starting phenix.real_space_refine on Thu Sep 26 10:52:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/09_2024/7wbu_32406.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/09_2024/7wbu_32406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/09_2024/7wbu_32406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/09_2024/7wbu_32406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/09_2024/7wbu_32406.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbu_32406/09_2024/7wbu_32406.cif" } resolution = 3.42 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7170 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 77 5.16 5 C 4558 2.51 5 N 1189 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7170 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7143 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 868} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.61 Number of scatterers: 7170 At special positions: 0 Unit cell: (84.66, 90.885, 117.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 2 15.00 O 1344 8.00 N 1189 7.00 C 4558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 834.4 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 3 sheets defined 57.1% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 97 through 112 removed outlier: 3.921A pdb=" N GLU A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 191 through 196 removed outlier: 4.075A pdb=" N GLY A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 303 through 315 Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.810A pdb=" N LYS A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 388 through 409 Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 449 through 461 removed outlier: 3.829A pdb=" N TYR A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 492 through 504 removed outlier: 3.833A pdb=" N THR A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 516 Processing helix chain 'A' and resid 522 through 537 Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.653A pdb=" N VAL A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 557 removed outlier: 3.761A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 615 through 633 removed outlier: 4.029A pdb=" N ALA A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 631 " --> pdb=" O CYS A 627 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 659 Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 703 through 715 Processing helix chain 'A' and resid 732 through 746 removed outlier: 3.989A pdb=" N ASP A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 816 through 829 removed outlier: 4.213A pdb=" N VAL A 821 " --> pdb=" O LYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 860 removed outlier: 3.546A pdb=" N ILE A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 858 " --> pdb=" O ALA A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 887 Processing helix chain 'A' and resid 905 through 915 removed outlier: 4.411A pdb=" N ASP A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 915 " --> pdb=" O ALA A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 944 Processing helix chain 'A' and resid 960 through 974 Processing helix chain 'A' and resid 984 through 993 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.035A pdb=" N PHE A 185 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE A 230 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE A 187 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASP A 232 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 189 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 278 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 152 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA3, first strand: chain 'A' and resid 571 through 576 removed outlier: 4.432A pdb=" N MET A 602 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 639 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASN A 671 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 641 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE A 668 " --> pdb=" O ASN A 696 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1089 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: 2.28 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1196 1.31 - 1.44: 1881 1.44 - 1.56: 4134 1.56 - 1.69: 5 1.69 - 1.82: 103 Bond restraints: 7319 Sorted by residual: bond pdb=" C ASN A 615 " pdb=" O ASN A 615 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.26e-02 6.30e+03 1.73e+01 bond pdb=" C LYS A 619 " pdb=" O LYS A 619 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.61e+01 bond pdb=" C GLU A 618 " pdb=" O GLU A 618 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.17e-02 7.31e+03 1.58e+01 bond pdb=" CA LYS A 619 " pdb=" C LYS A 619 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.27e-02 6.20e+03 1.52e+01 bond pdb=" N LYS A 619 " pdb=" CA LYS A 619 " ideal model delta sigma weight residual 1.459 1.425 0.035 1.19e-02 7.06e+03 8.52e+00 ... (remaining 7314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 9746 1.98 - 3.96: 113 3.96 - 5.95: 28 5.95 - 7.93: 9 7.93 - 9.91: 2 Bond angle restraints: 9898 Sorted by residual: angle pdb=" CA PRO A 98 " pdb=" N PRO A 98 " pdb=" CD PRO A 98 " ideal model delta sigma weight residual 112.00 102.09 9.91 1.40e+00 5.10e-01 5.01e+01 angle pdb=" CA PRO A 254 " pdb=" N PRO A 254 " pdb=" CD PRO A 254 " ideal model delta sigma weight residual 112.00 104.23 7.77 1.40e+00 5.10e-01 3.08e+01 angle pdb=" N ASN A 615 " pdb=" CA ASN A 615 " pdb=" CB ASN A 615 " ideal model delta sigma weight residual 110.49 119.62 -9.13 1.69e+00 3.50e-01 2.92e+01 angle pdb=" N THR A 616 " pdb=" CA THR A 616 " pdb=" C THR A 616 " ideal model delta sigma weight residual 111.28 116.43 -5.15 1.09e+00 8.42e-01 2.23e+01 angle pdb=" N GLU A 454 " pdb=" CA GLU A 454 " pdb=" CB GLU A 454 " ideal model delta sigma weight residual 110.39 116.67 -6.28 1.66e+00 3.63e-01 1.43e+01 ... (remaining 9893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 4192 26.27 - 52.54: 220 52.54 - 78.81: 16 78.81 - 105.08: 6 105.08 - 131.35: 2 Dihedral angle restraints: 4436 sinusoidal: 1793 harmonic: 2643 Sorted by residual: dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual 300.00 168.65 131.35 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual 300.00 176.19 123.81 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" N ASN A 615 " pdb=" C ASN A 615 " pdb=" CA ASN A 615 " pdb=" CB ASN A 615 " ideal model delta harmonic sigma weight residual 122.80 132.69 -9.89 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 4433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 967 0.055 - 0.110: 149 0.110 - 0.164: 11 0.164 - 0.219: 0 0.219 - 0.274: 3 Chirality restraints: 1130 Sorted by residual: chirality pdb=" CA THR A 616 " pdb=" N THR A 616 " pdb=" C THR A 616 " pdb=" CB THR A 616 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ASN A 615 " pdb=" N ASN A 615 " pdb=" C ASN A 615 " pdb=" CB ASN A 615 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PRO A 98 " pdb=" N PRO A 98 " pdb=" C PRO A 98 " pdb=" CB PRO A 98 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1127 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 253 " 0.096 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO A 254 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 97 " 0.065 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 98 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " -0.015 2.00e-02 2.50e+03 1.62e-02 6.56e+00 pdb=" CG TRP A 432 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " -0.000 2.00e-02 2.50e+03 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 126 2.70 - 3.25: 7093 3.25 - 3.80: 11243 3.80 - 4.35: 14609 4.35 - 4.90: 23944 Nonbonded interactions: 57015 Sorted by model distance: nonbonded pdb=" O VAL A 605 " pdb=" NZ LYS A 619 " model vdw 2.145 3.120 nonbonded pdb=" OD1 ASP A 875 " pdb=" OG SER A 906 " model vdw 2.249 3.040 nonbonded pdb=" NE1 TRP A 210 " pdb=" OG SER A 214 " model vdw 2.256 3.120 nonbonded pdb=" O LEU A 309 " pdb=" ND1 HIS A 313 " model vdw 2.308 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" O VAL A 186 " model vdw 2.327 3.040 ... (remaining 57010 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 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.200 Find NCS groups from input model: 0.060 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.003 0.144 7319 Z= 0.259 Angle : 0.590 9.912 9898 Z= 0.314 Chirality : 0.040 0.274 1130 Planarity : 0.006 0.140 1248 Dihedral : 15.373 131.352 2706 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.37 % Allowed : 0.24 % Favored : 99.39 % Cbeta Deviations : 0.12 % 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: 0.89 (0.29), residues: 894 helix: 1.57 (0.24), residues: 476 sheet: -0.68 (0.53), residues: 109 loop : -0.38 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 432 HIS 0.003 0.001 HIS A 887 PHE 0.017 0.001 PHE A 107 TYR 0.013 0.001 TYR A 139 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.851 Fit side-chains REVERT: A 417 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6996 (tm-30) REVERT: A 578 THR cc_start: 0.7833 (m) cc_final: 0.7528 (p) outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 0.1577 time to fit residues: 32.0956 Evaluate side-chains 103 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 287 ASN A 675 ASN A 678 ASN ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7319 Z= 0.175 Angle : 0.531 7.786 9898 Z= 0.267 Chirality : 0.038 0.137 1130 Planarity : 0.004 0.082 1248 Dihedral : 7.138 131.845 960 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.34 % Allowed : 8.30 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 894 helix: 1.67 (0.24), residues: 488 sheet: -0.78 (0.52), residues: 111 loop : -0.26 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 432 HIS 0.003 0.001 HIS A 313 PHE 0.021 0.001 PHE A 107 TYR 0.010 0.001 TYR A 288 ARG 0.004 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 124 TYR cc_start: 0.7488 (t80) cc_final: 0.6857 (t80) REVERT: A 417 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 581 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7337 (mp0) outliers start: 11 outliers final: 9 residues processed: 135 average time/residue: 0.1672 time to fit residues: 31.6087 Evaluate side-chains 113 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 803 ASN A 887 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7319 Z= 0.356 Angle : 0.652 7.861 9898 Z= 0.330 Chirality : 0.043 0.168 1130 Planarity : 0.005 0.067 1248 Dihedral : 7.617 142.235 957 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.56 % Allowed : 9.77 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 894 helix: 1.34 (0.23), residues: 487 sheet: -1.22 (0.51), residues: 114 loop : -0.46 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 179 HIS 0.005 0.001 HIS A 313 PHE 0.026 0.002 PHE A 325 TYR 0.014 0.002 TYR A 124 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.898 Fit side-chains REVERT: A 284 MET cc_start: 0.1761 (ttt) cc_final: 0.0928 (tmm) REVERT: A 581 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7315 (mp0) REVERT: A 725 MET cc_start: 0.7795 (mtt) cc_final: 0.7469 (mtt) REVERT: A 803 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.6849 (m-40) REVERT: A 843 CYS cc_start: 0.7040 (m) cc_final: 0.6668 (m) outliers start: 21 outliers final: 14 residues processed: 125 average time/residue: 0.1768 time to fit residues: 31.4434 Evaluate side-chains 107 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 593 HIS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 7.9990 chunk 42 optimal weight: 0.0470 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7319 Z= 0.239 Angle : 0.565 6.765 9898 Z= 0.287 Chirality : 0.040 0.150 1130 Planarity : 0.004 0.060 1248 Dihedral : 7.495 147.556 957 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.44 % Allowed : 12.94 % Favored : 84.62 % 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: 0.66 (0.28), residues: 894 helix: 1.46 (0.23), residues: 485 sheet: -1.31 (0.51), residues: 114 loop : -0.42 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 179 HIS 0.004 0.001 HIS A 155 PHE 0.025 0.002 PHE A 188 TYR 0.009 0.001 TYR A 698 ARG 0.008 0.001 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.994 Fit side-chains REVERT: A 284 MET cc_start: 0.1725 (ttt) cc_final: 0.0941 (tmm) REVERT: A 371 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 581 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7172 (mp0) REVERT: A 843 CYS cc_start: 0.7061 (m) cc_final: 0.6717 (m) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.1545 time to fit residues: 27.0747 Evaluate side-chains 108 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 593 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7319 Z= 0.286 Angle : 0.589 7.045 9898 Z= 0.301 Chirality : 0.041 0.153 1130 Planarity : 0.004 0.046 1248 Dihedral : 7.606 155.350 957 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.05 % Allowed : 14.65 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.28), residues: 894 helix: 1.38 (0.23), residues: 484 sheet: -1.23 (0.53), residues: 108 loop : -0.61 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 179 HIS 0.004 0.001 HIS A 155 PHE 0.020 0.002 PHE A 325 TYR 0.015 0.001 TYR A 124 ARG 0.003 0.000 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.917 Fit side-chains REVERT: A 284 MET cc_start: 0.1715 (ttt) cc_final: 0.0928 (tmm) REVERT: A 371 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8409 (tt) REVERT: A 474 ILE cc_start: 0.9308 (mt) cc_final: 0.9104 (mm) REVERT: A 581 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7304 (mp0) REVERT: A 599 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.8011 (t-90) REVERT: A 688 HIS cc_start: 0.4605 (OUTLIER) cc_final: 0.4308 (t-90) outliers start: 25 outliers final: 14 residues processed: 120 average time/residue: 0.1635 time to fit residues: 28.1359 Evaluate side-chains 110 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7319 Z= 0.207 Angle : 0.555 7.130 9898 Z= 0.282 Chirality : 0.039 0.152 1130 Planarity : 0.004 0.048 1248 Dihedral : 7.692 173.559 957 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.93 % Allowed : 15.75 % Favored : 81.32 % 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: 0.57 (0.28), residues: 894 helix: 1.42 (0.23), residues: 485 sheet: -1.33 (0.51), residues: 112 loop : -0.55 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 494 HIS 0.008 0.001 HIS A 599 PHE 0.022 0.001 PHE A 325 TYR 0.011 0.001 TYR A 124 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.885 Fit side-chains REVERT: A 284 MET cc_start: 0.1689 (ttt) cc_final: 0.0930 (tmm) REVERT: A 371 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 437 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7482 (mp) REVERT: A 459 MET cc_start: 0.7817 (tpp) cc_final: 0.7531 (tpp) REVERT: A 474 ILE cc_start: 0.9301 (mt) cc_final: 0.9085 (mm) REVERT: A 581 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7269 (mp0) REVERT: A 599 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.7861 (t-90) outliers start: 24 outliers final: 14 residues processed: 120 average time/residue: 0.1673 time to fit residues: 28.9214 Evaluate side-chains 107 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 HIS ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7319 Z= 0.294 Angle : 0.617 6.758 9898 Z= 0.313 Chirality : 0.041 0.155 1130 Planarity : 0.004 0.051 1248 Dihedral : 6.909 148.348 957 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.30 % Allowed : 16.61 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 894 helix: 1.30 (0.23), residues: 485 sheet: -1.35 (0.51), residues: 112 loop : -0.63 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 210 HIS 0.006 0.001 HIS A 599 PHE 0.022 0.002 PHE A 325 TYR 0.015 0.001 TYR A 124 ARG 0.003 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.853 Fit side-chains REVERT: A 124 TYR cc_start: 0.7818 (t80) cc_final: 0.7569 (t80) REVERT: A 371 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 437 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 599 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.7862 (t-90) REVERT: A 688 HIS cc_start: 0.4609 (OUTLIER) cc_final: 0.4310 (t-90) outliers start: 27 outliers final: 18 residues processed: 116 average time/residue: 0.1558 time to fit residues: 25.9197 Evaluate side-chains 112 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Chi-restraints excluded: chain A residue 977 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7319 Z= 0.207 Angle : 0.581 7.074 9898 Z= 0.292 Chirality : 0.039 0.153 1130 Planarity : 0.004 0.048 1248 Dihedral : 5.701 103.955 957 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.93 % Allowed : 17.09 % Favored : 79.98 % 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: 0.55 (0.29), residues: 894 helix: 1.40 (0.24), residues: 486 sheet: -1.38 (0.51), residues: 112 loop : -0.54 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 494 HIS 0.009 0.001 HIS A 599 PHE 0.023 0.001 PHE A 325 TYR 0.011 0.001 TYR A 124 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.795 Fit side-chains REVERT: A 124 TYR cc_start: 0.7614 (t80) cc_final: 0.7380 (t80) REVERT: A 284 MET cc_start: 0.1811 (ttt) cc_final: 0.0786 (tmm) REVERT: A 437 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7461 (mp) REVERT: A 459 MET cc_start: 0.7850 (tpp) cc_final: 0.7405 (tpp) REVERT: A 581 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6924 (mm-30) REVERT: A 599 HIS cc_start: 0.8483 (OUTLIER) cc_final: 0.7822 (t-90) outliers start: 24 outliers final: 16 residues processed: 115 average time/residue: 0.1608 time to fit residues: 26.6112 Evaluate side-chains 111 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Chi-restraints excluded: chain A residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7319 Z= 0.228 Angle : 0.608 11.808 9898 Z= 0.301 Chirality : 0.040 0.153 1130 Planarity : 0.004 0.091 1248 Dihedral : 5.697 103.735 957 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.93 % Allowed : 16.97 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 894 helix: 1.37 (0.24), residues: 486 sheet: -1.37 (0.51), residues: 112 loop : -0.55 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 494 HIS 0.003 0.001 HIS A 155 PHE 0.023 0.002 PHE A 325 TYR 0.012 0.001 TYR A 124 ARG 0.002 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.861 Fit side-chains REVERT: A 124 TYR cc_start: 0.7660 (t80) cc_final: 0.7423 (t80) REVERT: A 284 MET cc_start: 0.1827 (ttt) cc_final: 0.0822 (tmm) REVERT: A 371 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8442 (tt) REVERT: A 437 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 459 MET cc_start: 0.7761 (tpp) cc_final: 0.7282 (tpp) REVERT: A 599 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7954 (t-90) outliers start: 24 outliers final: 18 residues processed: 112 average time/residue: 0.1804 time to fit residues: 29.1157 Evaluate side-chains 113 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Chi-restraints excluded: chain A residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7319 Z= 0.180 Angle : 0.591 11.276 9898 Z= 0.292 Chirality : 0.039 0.152 1130 Planarity : 0.004 0.084 1248 Dihedral : 5.508 99.287 957 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.69 % Allowed : 17.46 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.29), residues: 894 helix: 1.43 (0.24), residues: 487 sheet: -1.41 (0.51), residues: 112 loop : -0.39 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 494 HIS 0.006 0.001 HIS A 599 PHE 0.026 0.001 PHE A 325 TYR 0.009 0.001 TYR A 124 ARG 0.002 0.000 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.917 Fit side-chains REVERT: A 284 MET cc_start: 0.1772 (ttt) cc_final: 0.0830 (tmm) REVERT: A 437 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7398 (mp) REVERT: A 459 MET cc_start: 0.7740 (tpp) cc_final: 0.7268 (tpp) REVERT: A 599 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7859 (t-90) outliers start: 22 outliers final: 18 residues processed: 107 average time/residue: 0.1595 time to fit residues: 24.5336 Evaluate side-chains 111 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Chi-restraints excluded: chain A residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.172573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.146792 restraints weight = 9854.419| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.59 r_work: 0.3686 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7319 Z= 0.144 Angle : 0.573 10.477 9898 Z= 0.281 Chirality : 0.038 0.148 1130 Planarity : 0.004 0.079 1248 Dihedral : 5.179 90.498 957 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.08 % Allowed : 17.95 % Favored : 79.98 % 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: 0.75 (0.29), residues: 894 helix: 1.51 (0.24), residues: 487 sheet: -1.51 (0.50), residues: 114 loop : -0.23 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 927 HIS 0.003 0.001 HIS A 599 PHE 0.022 0.001 PHE A 325 TYR 0.007 0.001 TYR A 698 ARG 0.002 0.000 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.52 seconds wall clock time: 29 minutes 48.35 seconds (1788.35 seconds total)