Starting phenix.real_space_refine on Sun Apr 27 12:45:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0b_36759/04_2025/8k0b_36759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0b_36759/04_2025/8k0b_36759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0b_36759/04_2025/8k0b_36759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0b_36759/04_2025/8k0b_36759.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0b_36759/04_2025/8k0b_36759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0b_36759/04_2025/8k0b_36759.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 34 5.16 5 C 3758 2.51 5 N 945 2.21 5 O 952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5689 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5689 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 25, 'TRANS': 663} Time building chain proxies: 3.92, per 1000 atoms: 0.69 Number of scatterers: 5689 At special positions: 0 Unit cell: (104.94, 93.28, 92.22, 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 34 16.00 O 952 8.00 N 945 7.00 C 3758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 300 " distance=2.03 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: 1.37 Conformation dependent library (CDL) restraints added in 632.7 milliseconds 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 64.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 35 through 61 Processing helix chain 'A' and resid 63 through 73 removed outlier: 4.353A pdb=" N ALA A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.619A pdb=" N LEU A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 removed outlier: 3.959A pdb=" N ALA A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 146 removed outlier: 3.653A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 140 " --> pdb=" O HIS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 182 through 206 Processing helix chain 'A' and resid 231 through 243 removed outlier: 4.030A pdb=" N ILE A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 285 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.944A pdb=" N ARG A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 334 removed outlier: 4.135A pdb=" N GLN A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 359 removed outlier: 3.725A pdb=" N VAL A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 406 through 429 Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 446 through 477 removed outlier: 4.132A pdb=" N PHE A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Proline residue: A 454 - end of helix Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 480 through 502 removed outlier: 3.968A pdb=" N TYR A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 540 through 560 removed outlier: 4.238A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 removed outlier: 3.833A pdb=" N CYS A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.777A pdb=" N VAL A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 617 through 640 removed outlier: 3.938A pdb=" N PHE A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 661 removed outlier: 3.950A pdb=" N HIS A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 656 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 677 removed outlier: 3.856A pdb=" N GLY A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 712 removed outlier: 3.696A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 692 " --> pdb=" O MET A 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 255 removed outlier: 5.716A pdb=" N LEU A 340 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 223 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A 382 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289 318 hydrogen bonds defined for protein. 939 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: 1.64 Time building geometry restraints manager: 1.61 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: 832 1.31 - 1.44: 1783 1.44 - 1.56: 3192 1.56 - 1.69: 0 1.69 - 1.82: 51 Bond restraints: 5858 Sorted by residual: bond pdb=" C TYR A 130 " pdb=" O TYR A 130 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.32e+01 bond pdb=" CA TYR A 130 " pdb=" C TYR A 130 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.32e+01 bond pdb=" CA SER A 687 " pdb=" CB SER A 687 " ideal model delta sigma weight residual 1.530 1.478 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" N TYR A 54 " pdb=" CA TYR A 54 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.82e+00 bond pdb=" N SER A 689 " pdb=" CA SER A 689 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.10e+00 ... (remaining 5853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 7860 3.25 - 6.51: 82 6.51 - 9.76: 14 9.76 - 13.01: 3 13.01 - 16.27: 2 Bond angle restraints: 7961 Sorted by residual: angle pdb=" C TYR A 130 " pdb=" CA TYR A 130 " pdb=" CB TYR A 130 " ideal model delta sigma weight residual 110.96 94.69 16.27 1.54e+00 4.22e-01 1.12e+02 angle pdb=" N HIS A 136 " pdb=" CA HIS A 136 " pdb=" C HIS A 136 " ideal model delta sigma weight residual 112.87 102.31 10.56 1.20e+00 6.94e-01 7.74e+01 angle pdb=" N SER A 687 " pdb=" CA SER A 687 " pdb=" C SER A 687 " ideal model delta sigma weight residual 111.11 101.72 9.39 1.20e+00 6.94e-01 6.12e+01 angle pdb=" C ILE A 131 " pdb=" N THR A 132 " pdb=" CA THR A 132 " ideal model delta sigma weight residual 120.79 111.26 9.53 1.39e+00 5.18e-01 4.70e+01 angle pdb=" C HIS A 136 " pdb=" CA HIS A 136 " pdb=" CB HIS A 136 " ideal model delta sigma weight residual 110.21 124.85 -14.64 2.19e+00 2.09e-01 4.47e+01 ... (remaining 7956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 2883 17.46 - 34.91: 389 34.91 - 52.37: 104 52.37 - 69.83: 22 69.83 - 87.29: 9 Dihedral angle restraints: 3407 sinusoidal: 1361 harmonic: 2046 Sorted by residual: dihedral pdb=" C TYR A 130 " pdb=" N TYR A 130 " pdb=" CA TYR A 130 " pdb=" CB TYR A 130 " ideal model delta harmonic sigma weight residual -122.60 -103.89 -18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" CA LEU A 536 " pdb=" C LEU A 536 " pdb=" N PRO A 537 " pdb=" CA PRO A 537 " ideal model delta harmonic sigma weight residual 180.00 147.47 32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 300 " pdb=" CB CYS A 300 " ideal model delta sinusoidal sigma weight residual 93.00 145.30 -52.30 1 1.00e+01 1.00e-02 3.73e+01 ... (remaining 3404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 737 0.057 - 0.114: 139 0.114 - 0.171: 11 0.171 - 0.228: 7 0.228 - 0.286: 2 Chirality restraints: 896 Sorted by residual: chirality pdb=" CA TYR A 130 " pdb=" N TYR A 130 " pdb=" C TYR A 130 " pdb=" CB TYR A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA HIS A 136 " pdb=" N HIS A 136 " pdb=" C HIS A 136 " pdb=" CB HIS A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA GLN A 134 " pdb=" N GLN A 134 " pdb=" C GLN A 134 " pdb=" CB GLN A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 893 not shown) Planarity restraints: 974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 128 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ARG A 128 " -0.068 2.00e-02 2.50e+03 pdb=" O ARG A 128 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A 129 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 671 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C PHE A 671 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE A 671 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 672 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 193 " -0.031 2.00e-02 2.50e+03 2.11e-02 8.87e+00 pdb=" CG TYR A 193 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 193 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 193 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 193 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 193 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 193 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 193 " -0.005 2.00e-02 2.50e+03 ... (remaining 971 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 439 2.74 - 3.28: 5992 3.28 - 3.82: 9520 3.82 - 4.36: 10716 4.36 - 4.90: 17742 Nonbonded interactions: 44409 Sorted by model distance: nonbonded pdb=" OD1 ASN A 636 " pdb=" OG SER A 640 " model vdw 2.195 3.040 nonbonded pdb=" O ASP A 520 " pdb=" NH1 ARG A 530 " model vdw 2.281 3.120 nonbonded pdb=" O PHE A 420 " pdb=" OG1 THR A 424 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASP A 339 " pdb=" NH2 ARG A 400 " model vdw 2.325 3.120 nonbonded pdb=" OG1 THR A 278 " pdb=" OE2 GLU A 312 " model vdw 2.338 3.040 ... (remaining 44404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.190 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 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 0.055 5859 Z= 0.230 Angle : 0.865 16.268 7963 Z= 0.506 Chirality : 0.047 0.286 896 Planarity : 0.005 0.057 974 Dihedral : 17.336 87.286 2080 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.28 % Allowed : 31.31 % Favored : 67.41 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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 (0.33), residues: 687 helix: 0.59 (0.27), residues: 398 sheet: 0.92 (1.28), residues: 17 loop : -2.07 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 479 HIS 0.003 0.001 HIS A 362 PHE 0.022 0.001 PHE A 519 TYR 0.049 0.002 TYR A 193 ARG 0.003 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.14938 ( 318) hydrogen bonds : angle 6.52307 ( 939) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.39721 ( 2) covalent geometry : bond 0.00373 ( 5858) covalent geometry : angle 0.86471 ( 7961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 131 ILE cc_start: 0.6800 (tt) cc_final: 0.6532 (tp) REVERT: A 221 MET cc_start: 0.4513 (tmm) cc_final: 0.3930 (ppp) REVERT: A 671 PHE cc_start: 0.7396 (t80) cc_final: 0.7137 (t80) REVERT: A 688 MET cc_start: 0.6435 (tpp) cc_final: 0.6142 (tpp) outliers start: 8 outliers final: 2 residues processed: 108 average time/residue: 0.1658 time to fit residues: 23.9448 Evaluate side-chains 106 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 691 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.0060 chunk 17 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 197 ASN A 593 GLN A 630 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.241147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.207568 restraints weight = 10896.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.211279 restraints weight = 5595.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.213704 restraints weight = 3634.221| |-----------------------------------------------------------------------------| r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5859 Z= 0.149 Angle : 0.662 12.636 7963 Z= 0.342 Chirality : 0.043 0.170 896 Planarity : 0.004 0.059 974 Dihedral : 5.418 55.136 766 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.71 % Allowed : 26.36 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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 (0.33), residues: 687 helix: 0.77 (0.27), residues: 404 sheet: 0.98 (1.33), residues: 17 loop : -2.07 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 668 HIS 0.005 0.001 HIS A 362 PHE 0.023 0.001 PHE A 140 TYR 0.040 0.002 TYR A 193 ARG 0.003 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 318) hydrogen bonds : angle 5.09793 ( 939) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.44696 ( 2) covalent geometry : bond 0.00309 ( 5858) covalent geometry : angle 0.66202 ( 7961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.4634 (tmm) cc_final: 0.4312 (ppp) REVERT: A 411 ILE cc_start: 0.7301 (tp) cc_final: 0.7046 (mt) REVERT: A 437 VAL cc_start: -0.2406 (OUTLIER) cc_final: -0.3144 (m) REVERT: A 522 TYR cc_start: 0.1202 (OUTLIER) cc_final: -0.0506 (m-80) REVERT: A 646 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.3849 (pp) REVERT: A 688 MET cc_start: 0.5458 (tpp) cc_final: 0.5218 (tpp) REVERT: A 690 SER cc_start: 0.7830 (t) cc_final: 0.7243 (p) outliers start: 42 outliers final: 23 residues processed: 141 average time/residue: 0.1548 time to fit residues: 29.6466 Evaluate side-chains 129 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 703 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 37 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 42 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.240867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.207285 restraints weight = 10852.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.211134 restraints weight = 5535.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.213658 restraints weight = 3584.448| |-----------------------------------------------------------------------------| r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5328 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5859 Z= 0.138 Angle : 0.666 15.276 7963 Z= 0.338 Chirality : 0.042 0.172 896 Planarity : 0.004 0.060 974 Dihedral : 5.102 46.233 766 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 7.51 % Allowed : 24.60 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.34 (0.33), residues: 687 helix: 0.85 (0.27), residues: 408 sheet: 1.01 (1.31), residues: 17 loop : -2.10 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 479 HIS 0.004 0.001 HIS A 362 PHE 0.025 0.001 PHE A 140 TYR 0.036 0.002 TYR A 193 ARG 0.002 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 318) hydrogen bonds : angle 4.95148 ( 939) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.48693 ( 2) covalent geometry : bond 0.00287 ( 5858) covalent geometry : angle 0.66589 ( 7961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.4514 (tmm) cc_final: 0.4302 (ppp) REVERT: A 411 ILE cc_start: 0.7287 (tp) cc_final: 0.7054 (mt) REVERT: A 433 ASP cc_start: 0.4404 (OUTLIER) cc_final: 0.3516 (p0) REVERT: A 437 VAL cc_start: -0.2293 (OUTLIER) cc_final: -0.3043 (m) REVERT: A 500 VAL cc_start: 0.7077 (p) cc_final: 0.6852 (p) REVERT: A 536 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6126 (mp) REVERT: A 565 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.2141 (mm) REVERT: A 598 TYR cc_start: 0.7480 (m-80) cc_final: 0.7132 (m-80) REVERT: A 604 VAL cc_start: 0.8237 (t) cc_final: 0.8004 (t) REVERT: A 608 VAL cc_start: 0.7798 (t) cc_final: 0.7546 (p) REVERT: A 646 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.3904 (pp) outliers start: 47 outliers final: 29 residues processed: 142 average time/residue: 0.1572 time to fit residues: 30.2637 Evaluate side-chains 133 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 713 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 28 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN A 657 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.240654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.206629 restraints weight = 11079.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.210585 restraints weight = 5646.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.213088 restraints weight = 3643.243| |-----------------------------------------------------------------------------| r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5344 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5859 Z= 0.137 Angle : 0.657 14.170 7963 Z= 0.334 Chirality : 0.042 0.171 896 Planarity : 0.004 0.059 974 Dihedral : 4.824 32.893 764 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 7.19 % Allowed : 25.88 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: 687 helix: 0.91 (0.27), residues: 406 sheet: 1.00 (1.28), residues: 17 loop : -2.02 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 668 HIS 0.004 0.001 HIS A 362 PHE 0.031 0.001 PHE A 140 TYR 0.035 0.002 TYR A 193 ARG 0.011 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 318) hydrogen bonds : angle 4.83360 ( 939) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.48020 ( 2) covalent geometry : bond 0.00288 ( 5858) covalent geometry : angle 0.65751 ( 7961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5588 (t80) cc_final: 0.5300 (t80) REVERT: A 209 VAL cc_start: 0.6937 (p) cc_final: 0.6124 (m) REVERT: A 411 ILE cc_start: 0.7305 (tp) cc_final: 0.7089 (mt) REVERT: A 433 ASP cc_start: 0.4355 (OUTLIER) cc_final: 0.3364 (p0) REVERT: A 437 VAL cc_start: -0.2351 (OUTLIER) cc_final: -0.3089 (m) REVERT: A 536 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.5924 (mt) REVERT: A 565 LEU cc_start: 0.1815 (OUTLIER) cc_final: 0.1588 (mm) REVERT: A 598 TYR cc_start: 0.7458 (m-80) cc_final: 0.6150 (m-80) REVERT: A 646 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.3971 (pp) REVERT: A 685 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.6130 (mm) outliers start: 45 outliers final: 28 residues processed: 138 average time/residue: 0.1600 time to fit residues: 29.9010 Evaluate side-chains 134 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.0000 chunk 27 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.239792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.205246 restraints weight = 10689.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.209245 restraints weight = 5490.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.211775 restraints weight = 3546.421| |-----------------------------------------------------------------------------| r_work (final): 0.4621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5383 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5859 Z= 0.152 Angle : 0.673 14.414 7963 Z= 0.341 Chirality : 0.043 0.169 896 Planarity : 0.004 0.061 974 Dihedral : 4.639 32.899 762 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.99 % Allowed : 25.72 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.33), residues: 687 helix: 0.77 (0.26), residues: 414 sheet: 0.66 (1.20), residues: 17 loop : -2.01 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 479 HIS 0.005 0.001 HIS A 362 PHE 0.028 0.001 PHE A 140 TYR 0.037 0.002 TYR A 193 ARG 0.006 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 318) hydrogen bonds : angle 4.88247 ( 939) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.47730 ( 2) covalent geometry : bond 0.00323 ( 5858) covalent geometry : angle 0.67307 ( 7961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.5908 (tpt) cc_final: 0.5689 (tmm) REVERT: A 133 PHE cc_start: 0.5576 (t80) cc_final: 0.5321 (t80) REVERT: A 411 ILE cc_start: 0.7312 (tp) cc_final: 0.7093 (mt) REVERT: A 433 ASP cc_start: 0.4184 (OUTLIER) cc_final: 0.3053 (p0) REVERT: A 437 VAL cc_start: -0.2381 (OUTLIER) cc_final: -0.3170 (m) REVERT: A 450 THR cc_start: 0.7490 (m) cc_final: 0.7267 (m) REVERT: A 522 TYR cc_start: 0.1318 (OUTLIER) cc_final: -0.0416 (m-80) REVERT: A 565 LEU cc_start: 0.1924 (OUTLIER) cc_final: 0.1515 (mm) REVERT: A 598 TYR cc_start: 0.7460 (m-80) cc_final: 0.5985 (m-80) REVERT: A 646 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.4393 (pp) REVERT: A 685 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6193 (mm) REVERT: A 690 SER cc_start: 0.7770 (t) cc_final: 0.7170 (p) outliers start: 50 outliers final: 31 residues processed: 140 average time/residue: 0.1553 time to fit residues: 29.3140 Evaluate side-chains 141 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.0050 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 = 0.4903 r_free = 0.4903 target = 0.240929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.206886 restraints weight = 10705.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.210923 restraints weight = 5563.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.213442 restraints weight = 3569.276| |-----------------------------------------------------------------------------| r_work (final): 0.4643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5332 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5859 Z= 0.129 Angle : 0.677 14.951 7963 Z= 0.338 Chirality : 0.042 0.161 896 Planarity : 0.004 0.059 974 Dihedral : 4.482 32.854 762 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 6.71 % Allowed : 28.12 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: 687 helix: 0.87 (0.27), residues: 413 sheet: 0.91 (1.22), residues: 17 loop : -2.00 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 668 HIS 0.003 0.001 HIS A 362 PHE 0.027 0.001 PHE A 140 TYR 0.033 0.002 TYR A 193 ARG 0.004 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 318) hydrogen bonds : angle 4.77702 ( 939) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.48152 ( 2) covalent geometry : bond 0.00273 ( 5858) covalent geometry : angle 0.67671 ( 7961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5574 (t80) cc_final: 0.5317 (t80) REVERT: A 193 TYR cc_start: 0.6464 (t80) cc_final: 0.5992 (t80) REVERT: A 406 THR cc_start: 0.7272 (p) cc_final: 0.7025 (t) REVERT: A 437 VAL cc_start: -0.2364 (OUTLIER) cc_final: -0.3110 (m) REVERT: A 512 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6630 (p-80) REVERT: A 522 TYR cc_start: 0.1409 (OUTLIER) cc_final: -0.0249 (m-80) REVERT: A 598 TYR cc_start: 0.7407 (m-80) cc_final: 0.5851 (m-80) REVERT: A 646 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.4256 (pp) REVERT: A 685 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6155 (mm) REVERT: A 690 SER cc_start: 0.7791 (t) cc_final: 0.7092 (p) outliers start: 42 outliers final: 28 residues processed: 131 average time/residue: 0.1762 time to fit residues: 31.0471 Evaluate side-chains 133 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.0870 chunk 46 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 0.0870 chunk 63 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 40.0000 chunk 2 optimal weight: 0.6980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.241248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.207477 restraints weight = 10860.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.211573 restraints weight = 5596.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.214159 restraints weight = 3582.292| |-----------------------------------------------------------------------------| r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5859 Z= 0.128 Angle : 0.675 14.542 7963 Z= 0.340 Chirality : 0.042 0.159 896 Planarity : 0.004 0.059 974 Dihedral : 4.463 32.603 762 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.03 % Allowed : 27.48 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: 687 helix: 0.92 (0.27), residues: 412 sheet: 1.01 (1.24), residues: 17 loop : -2.02 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 668 HIS 0.003 0.000 HIS A 362 PHE 0.027 0.001 PHE A 140 TYR 0.034 0.002 TYR A 193 ARG 0.009 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 318) hydrogen bonds : angle 4.72859 ( 939) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.47775 ( 2) covalent geometry : bond 0.00270 ( 5858) covalent geometry : angle 0.67528 ( 7961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5635 (t80) cc_final: 0.5358 (t80) REVERT: A 193 TYR cc_start: 0.6519 (t80) cc_final: 0.6012 (t80) REVERT: A 433 ASP cc_start: 0.4158 (OUTLIER) cc_final: 0.3161 (p0) REVERT: A 437 VAL cc_start: -0.2341 (OUTLIER) cc_final: -0.3050 (m) REVERT: A 500 VAL cc_start: 0.7111 (p) cc_final: 0.6904 (t) REVERT: A 512 HIS cc_start: 0.7153 (OUTLIER) cc_final: 0.6614 (p-80) REVERT: A 522 TYR cc_start: 0.1442 (OUTLIER) cc_final: -0.0302 (m-80) REVERT: A 534 VAL cc_start: 0.5240 (OUTLIER) cc_final: 0.5000 (m) REVERT: A 536 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.5875 (mt) REVERT: A 565 LEU cc_start: 0.1782 (OUTLIER) cc_final: 0.1579 (mm) REVERT: A 598 TYR cc_start: 0.7408 (m-80) cc_final: 0.5787 (m-80) REVERT: A 646 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.4371 (pp) REVERT: A 671 PHE cc_start: 0.7417 (t80) cc_final: 0.7124 (t80) REVERT: A 685 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6188 (mm) outliers start: 44 outliers final: 28 residues processed: 136 average time/residue: 0.1845 time to fit residues: 33.6307 Evaluate side-chains 136 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 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 583 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.238572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.204362 restraints weight = 10595.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.208139 restraints weight = 5506.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.210720 restraints weight = 3596.232| |-----------------------------------------------------------------------------| r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5405 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5859 Z= 0.166 Angle : 0.721 14.539 7963 Z= 0.366 Chirality : 0.044 0.166 896 Planarity : 0.005 0.061 974 Dihedral : 4.675 33.123 762 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 7.35 % Allowed : 27.64 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.40 (0.33), residues: 687 helix: 0.73 (0.26), residues: 412 sheet: 0.83 (1.20), residues: 17 loop : -2.02 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 479 HIS 0.005 0.001 HIS A 366 PHE 0.026 0.001 PHE A 140 TYR 0.038 0.002 TYR A 193 ARG 0.005 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 318) hydrogen bonds : angle 4.84267 ( 939) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.46368 ( 2) covalent geometry : bond 0.00357 ( 5858) covalent geometry : angle 0.72058 ( 7961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5641 (t80) cc_final: 0.5338 (t80) REVERT: A 172 THR cc_start: 0.7843 (t) cc_final: 0.7440 (p) REVERT: A 433 ASP cc_start: 0.4077 (OUTLIER) cc_final: 0.2898 (p0) REVERT: A 437 VAL cc_start: -0.2393 (OUTLIER) cc_final: -0.3245 (m) REVERT: A 522 TYR cc_start: 0.1209 (OUTLIER) cc_final: -0.0481 (m-80) REVERT: A 565 LEU cc_start: 0.1761 (OUTLIER) cc_final: 0.1490 (mm) REVERT: A 598 TYR cc_start: 0.7236 (m-80) cc_final: 0.5665 (m-80) REVERT: A 671 PHE cc_start: 0.7499 (t80) cc_final: 0.7029 (t80) REVERT: A 685 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6246 (mm) REVERT: A 690 SER cc_start: 0.7833 (t) cc_final: 0.7152 (p) outliers start: 46 outliers final: 33 residues processed: 136 average time/residue: 0.2128 time to fit residues: 39.1461 Evaluate side-chains 138 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 15 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 657 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.239078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.205255 restraints weight = 10606.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.209179 restraints weight = 5408.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.211702 restraints weight = 3492.983| |-----------------------------------------------------------------------------| r_work (final): 0.4618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5859 Z= 0.155 Angle : 0.739 14.659 7963 Z= 0.371 Chirality : 0.044 0.198 896 Planarity : 0.005 0.061 974 Dihedral : 4.660 33.410 762 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.55 % Allowed : 28.43 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.40 (0.33), residues: 687 helix: 0.71 (0.26), residues: 411 sheet: 0.84 (1.19), residues: 17 loop : -1.96 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 479 HIS 0.006 0.001 HIS A 651 PHE 0.027 0.001 PHE A 140 TYR 0.021 0.002 TYR A 193 ARG 0.005 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 318) hydrogen bonds : angle 4.88653 ( 939) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.46778 ( 2) covalent geometry : bond 0.00341 ( 5858) covalent geometry : angle 0.73935 ( 7961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.7938 (t) cc_final: 0.7523 (p) REVERT: A 197 ASN cc_start: 0.8356 (t0) cc_final: 0.8140 (t0) REVERT: A 433 ASP cc_start: 0.3906 (OUTLIER) cc_final: 0.2814 (p0) REVERT: A 437 VAL cc_start: -0.2348 (OUTLIER) cc_final: -0.3198 (m) REVERT: A 522 TYR cc_start: 0.1074 (OUTLIER) cc_final: -0.0583 (m-80) REVERT: A 598 TYR cc_start: 0.7293 (m-80) cc_final: 0.5736 (m-80) REVERT: A 671 PHE cc_start: 0.7605 (t80) cc_final: 0.7130 (t80) REVERT: A 685 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6215 (mm) REVERT: A 690 SER cc_start: 0.7837 (t) cc_final: 0.7133 (p) outliers start: 41 outliers final: 32 residues processed: 132 average time/residue: 0.1583 time to fit residues: 27.9668 Evaluate side-chains 138 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS A 583 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.238363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.204427 restraints weight = 10651.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.208442 restraints weight = 5425.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.210919 restraints weight = 3495.696| |-----------------------------------------------------------------------------| r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5859 Z= 0.180 Angle : 0.774 15.145 7963 Z= 0.390 Chirality : 0.046 0.196 896 Planarity : 0.005 0.060 974 Dihedral : 4.743 33.196 762 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 6.07 % Allowed : 28.75 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.33), residues: 687 helix: 0.57 (0.26), residues: 412 sheet: 0.76 (1.17), residues: 17 loop : -1.96 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 479 HIS 0.006 0.001 HIS A 651 PHE 0.026 0.001 PHE A 140 TYR 0.022 0.002 TYR A 315 ARG 0.005 0.001 ARG A 58 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 318) hydrogen bonds : angle 4.98320 ( 939) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.46241 ( 2) covalent geometry : bond 0.00393 ( 5858) covalent geometry : angle 0.77366 ( 7961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6955 (t) REVERT: A 172 THR cc_start: 0.7954 (t) cc_final: 0.7579 (p) REVERT: A 433 ASP cc_start: 0.3930 (OUTLIER) cc_final: 0.2801 (p0) REVERT: A 437 VAL cc_start: -0.2328 (OUTLIER) cc_final: -0.3208 (m) REVERT: A 522 TYR cc_start: 0.1110 (OUTLIER) cc_final: -0.0473 (m-80) REVERT: A 529 ILE cc_start: 0.2440 (OUTLIER) cc_final: 0.2195 (tt) REVERT: A 536 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.5925 (mt) REVERT: A 598 TYR cc_start: 0.7279 (m-80) cc_final: 0.5730 (m-80) REVERT: A 671 PHE cc_start: 0.7673 (t80) cc_final: 0.7174 (t80) REVERT: A 685 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6255 (mm) REVERT: A 690 SER cc_start: 0.7849 (t) cc_final: 0.7159 (p) outliers start: 38 outliers final: 28 residues processed: 126 average time/residue: 0.1782 time to fit residues: 30.6339 Evaluate side-chains 133 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 583 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.237625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.203592 restraints weight = 10629.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.207481 restraints weight = 5407.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.210097 restraints weight = 3497.239| |-----------------------------------------------------------------------------| r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5437 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5859 Z= 0.194 Angle : 0.783 15.209 7963 Z= 0.394 Chirality : 0.046 0.207 896 Planarity : 0.005 0.061 974 Dihedral : 4.814 34.656 762 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 6.23 % Allowed : 29.23 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.68 (0.33), residues: 687 helix: 0.45 (0.26), residues: 411 sheet: 0.74 (1.17), residues: 17 loop : -2.00 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 479 HIS 0.007 0.001 HIS A 366 PHE 0.025 0.001 PHE A 140 TYR 0.025 0.002 TYR A 193 ARG 0.005 0.001 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 318) hydrogen bonds : angle 5.03188 ( 939) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.45912 ( 2) covalent geometry : bond 0.00420 ( 5858) covalent geometry : angle 0.78276 ( 7961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.99 seconds wall clock time: 44 minutes 58.95 seconds (2698.95 seconds total)