Starting phenix.real_space_refine on Thu Jul 24 03:35:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n2e_48836/07_2025/9n2e_48836.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n2e_48836/07_2025/9n2e_48836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n2e_48836/07_2025/9n2e_48836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n2e_48836/07_2025/9n2e_48836.map" model { file = "/net/cci-nas-00/data/ceres_data/9n2e_48836/07_2025/9n2e_48836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n2e_48836/07_2025/9n2e_48836.cif" } resolution = 3.7 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= 0.013 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 7 5.16 5 C 3158 2.51 5 N 816 2.21 5 O 947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4928 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4501 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 561, 4493 Classifications: {'peptide': 561} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 541} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 561, 4493 Classifications: {'peptide': 561} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 541} Chain breaks: 7 bond proxies already assigned to first conformer: 4587 Chain: "E" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 427 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 11.74, per 1000 atoms: 2.38 Number of scatterers: 4928 At special positions: 0 Unit cell: (103.212, 72.468, 108.336, 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 7 16.00 O 947 8.00 N 816 7.00 C 3158 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: 1.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1110 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 4 sheets defined 16.8% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.585A pdb=" N LEU A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.870A pdb=" N GLU A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 removed outlier: 3.739A pdb=" N GLY A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 522 removed outlier: 4.479A pdb=" N LYS A 522 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 4.068A pdb=" N PHE A 640 " --> pdb=" O PRO A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 655 removed outlier: 6.661A pdb=" N LYS A 652 " --> pdb=" O GLN A 649 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU A 653 " --> pdb=" O ASN A 650 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A 655 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 658 No H-bonds generated for 'chain 'A' and resid 658 through 658' Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 156 through 166 Processing sheet with id=AA1, first strand: chain 'A' and resid 285 through 292 removed outlier: 6.532A pdb=" N TYR A 285 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N PHE A 362 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLY A 287 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ILE A 364 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N ILE A 289 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N ILE A 366 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N PHE A 291 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A 354 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU A 363 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU A 352 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG A 365 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA A 350 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR A 367 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 380 removed outlier: 5.889A pdb=" N VAL A 439 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS A 376 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 441 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR A 438 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL A 432 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 154 through 155 removed outlier: 3.581A pdb=" N ILE A 896 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 827 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 624 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 11.659A pdb=" N ARG A 548 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 12.346A pdb=" N ASN A 540 " --> pdb=" O ARG A 548 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN A 550 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 761 removed outlier: 7.177A pdb=" N TYR A 760 " --> pdb=" O ILE A 777 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 220 hydrogen bonds defined for protein. 608 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: 1.59 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1572 1.34 - 1.46: 1314 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 5039 Sorted by residual: bond pdb=" N GLY A 731 " pdb=" CA GLY A 731 " ideal model delta sigma weight residual 1.460 1.448 0.012 1.26e-02 6.30e+03 9.66e-01 bond pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta sigma weight residual 1.535 1.554 -0.019 1.93e-02 2.68e+03 9.53e-01 bond pdb=" CA GLY A 731 " pdb=" C GLY A 731 " ideal model delta sigma weight residual 1.524 1.511 0.012 1.33e-02 5.65e+03 8.49e-01 bond pdb=" CB GLU A 740 " pdb=" CG GLU A 740 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.36e-01 bond pdb=" CB MET A 491 " pdb=" CG MET A 491 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.06e-01 ... (remaining 5034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 6679 2.00 - 4.01: 102 4.01 - 6.01: 12 6.01 - 8.02: 4 8.02 - 10.02: 1 Bond angle restraints: 6798 Sorted by residual: angle pdb=" N ILE A 819 " pdb=" CA ILE A 819 " pdb=" C ILE A 819 " ideal model delta sigma weight residual 112.96 108.99 3.97 1.00e+00 1.00e+00 1.58e+01 angle pdb=" CB MET A 491 " pdb=" CG MET A 491 " pdb=" SD MET A 491 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" N VAL A 692 " pdb=" CA VAL A 692 " pdb=" C VAL A 692 " ideal model delta sigma weight residual 111.88 108.60 3.28 1.06e+00 8.90e-01 9.60e+00 angle pdb=" N GLN E 136 " pdb=" CA GLN E 136 " pdb=" C GLN E 136 " ideal model delta sigma weight residual 110.61 113.80 -3.19 1.25e+00 6.40e-01 6.51e+00 angle pdb=" CA MET A 491 " pdb=" CB MET A 491 " pdb=" CG MET A 491 " ideal model delta sigma weight residual 114.10 118.93 -4.83 2.00e+00 2.50e-01 5.84e+00 ... (remaining 6793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2488 17.85 - 35.71: 335 35.71 - 53.56: 89 53.56 - 71.41: 25 71.41 - 89.26: 8 Dihedral angle restraints: 2945 sinusoidal: 1181 harmonic: 1764 Sorted by residual: dihedral pdb=" CA GLN E 136 " pdb=" C GLN E 136 " pdb=" N SER E 137 " pdb=" CA SER E 137 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP E 134 " pdb=" C ASP E 134 " pdb=" N ARG E 135 " pdb=" CA ARG E 135 " ideal model delta harmonic sigma weight residual 180.00 -162.70 -17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA THR A 367 " pdb=" C THR A 367 " pdb=" N GLU A 368 " pdb=" CA GLU A 368 " ideal model delta harmonic sigma weight residual -180.00 -163.45 -16.55 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 410 0.032 - 0.064: 196 0.064 - 0.096: 62 0.096 - 0.128: 40 0.128 - 0.160: 3 Chirality restraints: 711 Sorted by residual: chirality pdb=" CB ILE A 643 " pdb=" CA ILE A 643 " pdb=" CG1 ILE A 643 " pdb=" CG2 ILE A 643 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA ILE A 377 " pdb=" N ILE A 377 " pdb=" C ILE A 377 " pdb=" CB ILE A 377 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA GLN E 136 " pdb=" N GLN E 136 " pdb=" C GLN E 136 " pdb=" CB GLN E 136 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 708 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 426 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 427 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 299 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" CG ASP A 299 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP A 299 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 299 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 516 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 517 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.022 5.00e-02 4.00e+02 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 2517 3.00 - 3.47: 4520 3.47 - 3.95: 7381 3.95 - 4.42: 8672 4.42 - 4.90: 14822 Nonbonded interactions: 37912 Sorted by model distance: nonbonded pdb=" O ASN A 336 " pdb=" ND2 ASN A 336 " model vdw 2.520 3.120 nonbonded pdb=" C THR A 678 " pdb=" OG1 THR A 678 " model vdw 2.520 2.616 nonbonded pdb=" N ASP E 134 " pdb=" OD1 ASP E 134 " model vdw 2.529 3.120 nonbonded pdb=" C THR A 556 " pdb=" OG1 THR A 556 " model vdw 2.539 2.616 nonbonded pdb=" N THR A 556 " pdb=" CG2 THR A 556 " model vdw 2.571 2.832 ... (remaining 37907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1786.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 27.870 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:4.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1818.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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 : 0.004 0.027 5039 Z= 0.167 Angle : 0.650 10.021 6798 Z= 0.361 Chirality : 0.045 0.160 711 Planarity : 0.004 0.045 881 Dihedral : 18.285 89.263 1835 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.59 % Allowed : 34.03 % Favored : 62.38 % 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: -0.02 (0.34), residues: 596 helix: 0.47 (0.53), residues: 81 sheet: 1.12 (0.35), residues: 212 loop : -1.00 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 890 HIS 0.003 0.001 HIS A 582 PHE 0.017 0.001 PHE A 552 TYR 0.014 0.001 TYR A 373 ARG 0.007 0.001 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.11095 ( 220) hydrogen bonds : angle 5.57513 ( 608) covalent geometry : bond 0.00361 ( 5039) covalent geometry : angle 0.65018 ( 6798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 362 PHE cc_start: 0.7654 (m-80) cc_final: 0.7393 (m-10) REVERT: A 512 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 532 SER cc_start: 0.8201 (m) cc_final: 0.7812 (t) REVERT: A 606 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7428 (p) REVERT: A 721 PHE cc_start: 0.6776 (t80) cc_final: 0.6552 (t80) REVERT: A 772 ASP cc_start: 0.7507 (p0) cc_final: 0.6942 (t0) REVERT: A 816 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.6928 (mtm180) outliers start: 19 outliers final: 12 residues processed: 114 average time/residue: 0.2304 time to fit residues: 32.7571 Evaluate side-chains 112 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 157 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 341 ASN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126273 restraints weight = 13841.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131530 restraints weight = 5704.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134655 restraints weight = 3108.251| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5039 Z= 0.237 Angle : 0.636 7.774 6798 Z= 0.337 Chirality : 0.047 0.166 711 Planarity : 0.004 0.047 881 Dihedral : 8.603 59.883 711 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.24 % Allowed : 30.43 % Favored : 63.33 % 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: -0.22 (0.34), residues: 596 helix: 0.21 (0.53), residues: 82 sheet: 0.98 (0.34), residues: 213 loop : -1.11 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 890 HIS 0.006 0.002 HIS A 582 PHE 0.027 0.002 PHE A 552 TYR 0.018 0.002 TYR A 874 ARG 0.005 0.001 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 220) hydrogen bonds : angle 5.24754 ( 608) covalent geometry : bond 0.00543 ( 5039) covalent geometry : angle 0.63616 ( 6798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 354 LYS cc_start: 0.7624 (ttmm) cc_final: 0.7396 (tptt) REVERT: A 430 ARG cc_start: 0.7216 (mmt180) cc_final: 0.6990 (mmm-85) REVERT: A 512 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7993 (tt) REVERT: A 532 SER cc_start: 0.8300 (m) cc_final: 0.7880 (t) REVERT: A 788 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8274 (p) REVERT: E 134 ASP cc_start: 0.7737 (p0) cc_final: 0.7488 (p0) REVERT: E 136 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7858 (pp30) outliers start: 33 outliers final: 22 residues processed: 123 average time/residue: 0.1866 time to fit residues: 28.8584 Evaluate side-chains 124 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 157 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 45 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 502 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130289 restraints weight = 8859.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134495 restraints weight = 4262.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137251 restraints weight = 2570.357| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5039 Z= 0.164 Angle : 0.587 6.699 6798 Z= 0.310 Chirality : 0.045 0.144 711 Planarity : 0.004 0.044 881 Dihedral : 8.050 59.560 702 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.29 % Allowed : 31.38 % Favored : 63.33 % 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: -0.11 (0.34), residues: 596 helix: 0.28 (0.54), residues: 82 sheet: 1.08 (0.35), residues: 213 loop : -1.05 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 518 HIS 0.004 0.001 HIS A 582 PHE 0.021 0.002 PHE A 552 TYR 0.012 0.001 TYR A 874 ARG 0.004 0.000 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 220) hydrogen bonds : angle 5.07495 ( 608) covalent geometry : bond 0.00374 ( 5039) covalent geometry : angle 0.58718 ( 6798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 PHE cc_start: 0.7674 (m-80) cc_final: 0.7302 (m-10) REVERT: A 512 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7981 (tt) REVERT: A 532 SER cc_start: 0.8284 (m) cc_final: 0.7879 (t) REVERT: A 606 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7400 (p) REVERT: A 788 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8266 (p) REVERT: E 134 ASP cc_start: 0.7794 (p0) cc_final: 0.7587 (p0) outliers start: 28 outliers final: 16 residues processed: 121 average time/residue: 0.3186 time to fit residues: 50.0932 Evaluate side-chains 118 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 149 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122012 restraints weight = 14348.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127205 restraints weight = 5930.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130558 restraints weight = 3236.235| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5039 Z= 0.235 Angle : 0.635 7.310 6798 Z= 0.335 Chirality : 0.047 0.132 711 Planarity : 0.004 0.047 881 Dihedral : 8.191 59.947 701 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 7.18 % Allowed : 29.87 % Favored : 62.95 % 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: -0.26 (0.34), residues: 596 helix: 0.16 (0.54), residues: 82 sheet: 1.03 (0.35), residues: 213 loop : -1.19 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 890 HIS 0.006 0.002 HIS A 582 PHE 0.025 0.002 PHE A 552 TYR 0.017 0.002 TYR A 874 ARG 0.004 0.001 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 220) hydrogen bonds : angle 5.24939 ( 608) covalent geometry : bond 0.00539 ( 5039) covalent geometry : angle 0.63504 ( 6798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7083 (tm-30) REVERT: A 496 LYS cc_start: 0.7202 (mtmm) cc_final: 0.6923 (mtmm) REVERT: A 512 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7969 (tt) REVERT: A 532 SER cc_start: 0.8313 (m) cc_final: 0.7914 (t) REVERT: A 726 TYR cc_start: 0.7714 (m-80) cc_final: 0.7424 (m-80) REVERT: A 788 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8282 (p) REVERT: A 816 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6674 (mtm180) REVERT: E 134 ASP cc_start: 0.7860 (p0) cc_final: 0.7468 (p0) outliers start: 38 outliers final: 23 residues processed: 132 average time/residue: 0.3053 time to fit residues: 51.2530 Evaluate side-chains 129 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 149 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123977 restraints weight = 11258.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128599 restraints weight = 5129.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131460 restraints weight = 2970.620| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5039 Z= 0.217 Angle : 0.631 6.557 6798 Z= 0.335 Chirality : 0.046 0.138 711 Planarity : 0.004 0.045 881 Dihedral : 8.180 59.838 701 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.43 % Allowed : 31.19 % Favored : 62.38 % 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: -0.27 (0.34), residues: 596 helix: 0.17 (0.55), residues: 82 sheet: 1.06 (0.35), residues: 209 loop : -1.21 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 890 HIS 0.006 0.001 HIS A 582 PHE 0.024 0.002 PHE A 552 TYR 0.015 0.002 TYR A 874 ARG 0.003 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 220) hydrogen bonds : angle 5.22475 ( 608) covalent geometry : bond 0.00496 ( 5039) covalent geometry : angle 0.63134 ( 6798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6612 (mt-10) REVERT: A 393 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7135 (tm-30) REVERT: A 430 ARG cc_start: 0.6880 (mmm-85) cc_final: 0.5669 (mmm-85) REVERT: A 496 LYS cc_start: 0.7190 (mtmm) cc_final: 0.6935 (mtmm) REVERT: A 512 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7979 (tt) REVERT: A 532 SER cc_start: 0.8333 (m) cc_final: 0.7945 (t) REVERT: A 649 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: A 726 TYR cc_start: 0.7676 (m-80) cc_final: 0.7418 (m-80) REVERT: A 788 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8271 (p) REVERT: A 816 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.6656 (mtm180) REVERT: E 134 ASP cc_start: 0.7871 (p0) cc_final: 0.7486 (p0) outliers start: 34 outliers final: 27 residues processed: 127 average time/residue: 0.1842 time to fit residues: 29.5913 Evaluate side-chains 129 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 893 HIS Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 157 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 58 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120655 restraints weight = 19082.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126394 restraints weight = 7210.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130109 restraints weight = 3765.308| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5039 Z= 0.190 Angle : 0.619 7.461 6798 Z= 0.329 Chirality : 0.046 0.129 711 Planarity : 0.004 0.043 881 Dihedral : 8.124 59.694 701 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 6.62 % Allowed : 30.62 % Favored : 62.76 % 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: -0.25 (0.34), residues: 596 helix: 0.25 (0.55), residues: 82 sheet: 1.01 (0.35), residues: 211 loop : -1.18 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 890 HIS 0.005 0.001 HIS A 582 PHE 0.022 0.002 PHE A 552 TYR 0.013 0.002 TYR A 874 ARG 0.003 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 220) hydrogen bonds : angle 5.18580 ( 608) covalent geometry : bond 0.00431 ( 5039) covalent geometry : angle 0.61858 ( 6798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 363 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6626 (mt-10) REVERT: A 430 ARG cc_start: 0.6815 (mmm-85) cc_final: 0.5769 (mmm-85) REVERT: A 496 LYS cc_start: 0.7155 (mtmm) cc_final: 0.6917 (mtmm) REVERT: A 512 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7980 (tt) REVERT: A 532 SER cc_start: 0.8340 (m) cc_final: 0.7882 (p) REVERT: A 606 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7377 (p) REVERT: A 649 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7767 (mm-40) REVERT: A 726 TYR cc_start: 0.7671 (m-80) cc_final: 0.7380 (m-80) REVERT: A 788 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 816 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6668 (mtm180) REVERT: A 853 SER cc_start: 0.7505 (p) cc_final: 0.7096 (p) REVERT: E 136 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8041 (pp30) outliers start: 35 outliers final: 26 residues processed: 126 average time/residue: 0.1823 time to fit residues: 29.2082 Evaluate side-chains 130 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 893 HIS Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 149 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 34 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 overall best weight: 0.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.147860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125162 restraints weight = 14250.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130430 restraints weight = 5950.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133813 restraints weight = 3270.823| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5039 Z= 0.105 Angle : 0.589 8.310 6798 Z= 0.312 Chirality : 0.044 0.129 711 Planarity : 0.004 0.043 881 Dihedral : 7.588 59.810 701 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.35 % Allowed : 33.08 % Favored : 62.57 % 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: -0.03 (0.35), residues: 596 helix: 0.41 (0.56), residues: 84 sheet: 1.24 (0.35), residues: 210 loop : -1.10 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 713 HIS 0.002 0.001 HIS A 582 PHE 0.015 0.001 PHE A 552 TYR 0.009 0.001 TYR A 828 ARG 0.002 0.000 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 220) hydrogen bonds : angle 4.94942 ( 608) covalent geometry : bond 0.00227 ( 5039) covalent geometry : angle 0.58858 ( 6798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 363 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6523 (mt-10) REVERT: A 504 SER cc_start: 0.8713 (t) cc_final: 0.8283 (m) REVERT: A 512 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7985 (tt) REVERT: A 532 SER cc_start: 0.8296 (m) cc_final: 0.7927 (p) REVERT: A 726 TYR cc_start: 0.7638 (m-80) cc_final: 0.7420 (m-80) REVERT: A 816 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6759 (mtm180) REVERT: E 136 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8061 (pp30) outliers start: 23 outliers final: 17 residues processed: 119 average time/residue: 0.1794 time to fit residues: 27.1625 Evaluate side-chains 115 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 157 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 8 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.0030 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 chunk 35 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.146415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125381 restraints weight = 11277.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130083 restraints weight = 5085.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133095 restraints weight = 2925.816| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5039 Z= 0.128 Angle : 0.596 8.834 6798 Z= 0.312 Chirality : 0.044 0.129 711 Planarity : 0.004 0.044 881 Dihedral : 7.352 59.727 700 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.16 % Allowed : 33.84 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.35), residues: 596 helix: 0.42 (0.55), residues: 84 sheet: 1.35 (0.35), residues: 210 loop : -1.12 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 890 HIS 0.003 0.001 HIS A 582 PHE 0.018 0.001 PHE A 552 TYR 0.012 0.001 TYR A 817 ARG 0.002 0.000 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.02657 ( 220) hydrogen bonds : angle 4.83878 ( 608) covalent geometry : bond 0.00285 ( 5039) covalent geometry : angle 0.59637 ( 6798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.5834 (mp10) REVERT: A 363 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6518 (mt-10) REVERT: A 512 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7960 (tt) REVERT: A 532 SER cc_start: 0.8309 (m) cc_final: 0.7908 (p) REVERT: A 726 TYR cc_start: 0.7664 (m-80) cc_final: 0.7425 (m-80) REVERT: A 788 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 816 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.6807 (mtm180) REVERT: A 853 SER cc_start: 0.7520 (p) cc_final: 0.7116 (p) REVERT: E 136 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8065 (pp30) REVERT: E 144 MET cc_start: 0.6267 (mtt) cc_final: 0.5935 (mtt) outliers start: 22 outliers final: 17 residues processed: 119 average time/residue: 0.1773 time to fit residues: 26.8292 Evaluate side-chains 118 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 157 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125904 restraints weight = 9152.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130073 restraints weight = 4382.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132857 restraints weight = 2610.014| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5039 Z= 0.162 Angle : 0.632 9.638 6798 Z= 0.332 Chirality : 0.045 0.130 711 Planarity : 0.004 0.046 881 Dihedral : 7.345 59.443 700 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.35 % Allowed : 34.59 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.35), residues: 596 helix: 0.40 (0.55), residues: 84 sheet: 1.23 (0.35), residues: 214 loop : -1.13 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 890 HIS 0.004 0.001 HIS A 582 PHE 0.021 0.001 PHE A 552 TYR 0.012 0.001 TYR A 828 ARG 0.002 0.000 ARG A 852 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 220) hydrogen bonds : angle 4.97037 ( 608) covalent geometry : bond 0.00367 ( 5039) covalent geometry : angle 0.63239 ( 6798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.5796 (mp10) REVERT: A 512 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7955 (tt) REVERT: A 532 SER cc_start: 0.8305 (m) cc_final: 0.7853 (p) REVERT: A 579 SER cc_start: 0.8255 (m) cc_final: 0.7798 (p) REVERT: A 606 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 726 TYR cc_start: 0.7661 (m-80) cc_final: 0.7391 (m-80) REVERT: A 772 ASP cc_start: 0.7510 (p0) cc_final: 0.7096 (t0) REVERT: A 788 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 816 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.6761 (mtm180) REVERT: A 853 SER cc_start: 0.7533 (p) cc_final: 0.7132 (p) REVERT: E 136 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8060 (pp30) REVERT: E 144 MET cc_start: 0.6426 (mtt) cc_final: 0.6092 (mtt) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.1736 time to fit residues: 25.9503 Evaluate side-chains 120 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.0170 chunk 43 optimal weight: 0.1980 chunk 59 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 0.0980 overall best weight: 0.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.148648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127408 restraints weight = 11289.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132172 restraints weight = 5096.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135215 restraints weight = 2942.460| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5039 Z= 0.096 Angle : 0.589 9.540 6798 Z= 0.307 Chirality : 0.043 0.129 711 Planarity : 0.004 0.045 881 Dihedral : 6.896 59.880 699 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.59 % Allowed : 34.78 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.35), residues: 596 helix: 0.70 (0.56), residues: 84 sheet: 1.46 (0.35), residues: 210 loop : -1.10 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 518 HIS 0.001 0.000 HIS A 582 PHE 0.014 0.001 PHE A 552 TYR 0.011 0.001 TYR A 828 ARG 0.002 0.000 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.02328 ( 220) hydrogen bonds : angle 4.65247 ( 608) covalent geometry : bond 0.00209 ( 5039) covalent geometry : angle 0.58940 ( 6798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5686 (mp10) REVERT: A 504 SER cc_start: 0.8698 (t) cc_final: 0.8291 (m) REVERT: A 512 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 532 SER cc_start: 0.8179 (m) cc_final: 0.7856 (t) REVERT: A 726 TYR cc_start: 0.7676 (m-80) cc_final: 0.7462 (m-80) REVERT: A 772 ASP cc_start: 0.7510 (p0) cc_final: 0.7070 (t0) REVERT: A 788 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8258 (p) REVERT: A 816 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6809 (mtm180) REVERT: E 144 MET cc_start: 0.6256 (mtt) cc_final: 0.5999 (mtt) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.1746 time to fit residues: 24.8461 Evaluate side-chains 109 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 0.0020 chunk 59 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 24 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123459 restraints weight = 14307.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128760 restraints weight = 5933.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132187 restraints weight = 3219.830| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5039 Z= 0.135 Angle : 0.604 9.462 6798 Z= 0.316 Chirality : 0.044 0.129 711 Planarity : 0.004 0.045 881 Dihedral : 6.876 59.113 698 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.35 % Allowed : 34.97 % Favored : 60.68 % 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: 0.14 (0.35), residues: 596 helix: 0.63 (0.55), residues: 85 sheet: 1.44 (0.35), residues: 210 loop : -1.12 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 890 HIS 0.003 0.001 HIS A 582 PHE 0.019 0.001 PHE A 552 TYR 0.011 0.001 TYR A 828 ARG 0.002 0.000 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.02681 ( 220) hydrogen bonds : angle 4.76751 ( 608) covalent geometry : bond 0.00304 ( 5039) covalent geometry : angle 0.60440 ( 6798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5538.06 seconds wall clock time: 100 minutes 30.14 seconds (6030.14 seconds total)