Starting phenix.real_space_refine on Tue Feb 3 12:53:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9naq_49201/02_2026/9naq_49201.cif Found real_map, /net/cci-nas-00/data/ceres_data/9naq_49201/02_2026/9naq_49201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9naq_49201/02_2026/9naq_49201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9naq_49201/02_2026/9naq_49201.map" model { file = "/net/cci-nas-00/data/ceres_data/9naq_49201/02_2026/9naq_49201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9naq_49201/02_2026/9naq_49201.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 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 12 5.16 5 C 1596 2.51 5 N 435 2.21 5 O 478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2521 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 837 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 759 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain breaks: 3 Time building chain proxies: 0.56, per 1000 atoms: 0.22 Number of scatterers: 2521 At special positions: 0 Unit cell: (52.2, 62.35, 81.2, 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 12 16.00 O 478 8.00 N 435 7.00 C 1596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 0.11 Conformation dependent library (CDL) restraints added in 56.6 milliseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 586 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 24.8% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 576 through 598 Processing helix chain 'A' and resid 620 through 636 removed outlier: 4.146A pdb=" N GLU A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.961A pdb=" N GLU A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 659' Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.996A pdb=" N LYS A 667 " --> pdb=" O HIS A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 removed outlier: 3.568A pdb=" N MET A 678 " --> pdb=" O TRP A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 714 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.096A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.785A pdb=" N THR L 105 " --> pdb=" O GLU L 11 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.785A pdb=" N THR L 105 " --> pdb=" O GLU L 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 20 107 hydrogen bonds defined for protein. 270 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: 0.42 Time building geometry restraints manager: 0.15 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: 803 1.34 - 1.45: 419 1.45 - 1.57: 1335 1.57 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 2576 Sorted by residual: bond pdb=" CG LEU L 46 " pdb=" CD1 LEU L 46 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.38e+00 bond pdb=" CG MET H 53 " pdb=" SD MET H 53 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CB MET A 665 " pdb=" CG MET A 665 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.76e-01 bond pdb=" CG LEU L 46 " pdb=" CD2 LEU L 46 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.14e-01 bond pdb=" CB ILE H 57 " pdb=" CG2 ILE H 57 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.77e-01 ... (remaining 2571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 3247 1.11 - 2.22: 193 2.22 - 3.34: 30 3.34 - 4.45: 8 4.45 - 5.56: 4 Bond angle restraints: 3482 Sorted by residual: angle pdb=" CG MET H 53 " pdb=" SD MET H 53 " pdb=" CE MET H 53 " ideal model delta sigma weight residual 100.90 95.65 5.25 2.20e+00 2.07e-01 5.69e+00 angle pdb=" CA ARG H 83 " pdb=" CB ARG H 83 " pdb=" CG ARG H 83 " ideal model delta sigma weight residual 114.10 118.42 -4.32 2.00e+00 2.50e-01 4.66e+00 angle pdb=" C ARG H 83 " pdb=" CA ARG H 83 " pdb=" CB ARG H 83 " ideal model delta sigma weight residual 109.79 114.21 -4.42 2.05e+00 2.38e-01 4.64e+00 angle pdb=" N ASP L 82 " pdb=" CA ASP L 82 " pdb=" C ASP L 82 " ideal model delta sigma weight residual 112.25 109.79 2.46 1.36e+00 5.41e-01 3.26e+00 angle pdb=" CA ASP H 55 " pdb=" CB ASP H 55 " pdb=" CG ASP H 55 " ideal model delta sigma weight residual 112.60 114.37 -1.77 1.00e+00 1.00e+00 3.14e+00 ... (remaining 3477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 1318 15.61 - 31.22: 134 31.22 - 46.84: 47 46.84 - 62.45: 7 62.45 - 78.06: 6 Dihedral angle restraints: 1512 sinusoidal: 603 harmonic: 909 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 140.51 -47.51 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CA MET H 100E" pdb=" C MET H 100E" pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta harmonic sigma weight residual -180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN A 633 " pdb=" C ASN A 633 " pdb=" N SER A 634 " pdb=" CA SER A 634 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 1509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 261 0.042 - 0.083: 95 0.083 - 0.125: 20 0.125 - 0.166: 4 0.166 - 0.208: 1 Chirality restraints: 381 Sorted by residual: chirality pdb=" CB THR H 108 " pdb=" CA THR H 108 " pdb=" OG1 THR H 108 " pdb=" CG2 THR H 108 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE H 89 " pdb=" CA ILE H 89 " pdb=" CG1 ILE H 89 " pdb=" CG2 ILE H 89 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 378 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 659 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C SER A 659 " 0.025 2.00e-02 2.50e+03 pdb=" O SER A 659 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE A 660 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 82 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C ASP L 82 " 0.021 2.00e-02 2.50e+03 pdb=" O ASP L 82 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU L 83 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 55 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" CG ASP H 55 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP H 55 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP H 55 " -0.007 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 59 2.68 - 3.24: 2339 3.24 - 3.79: 3879 3.79 - 4.35: 5299 4.35 - 4.90: 8667 Nonbonded interactions: 20243 Sorted by model distance: nonbonded pdb=" OD1 ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.129 3.040 nonbonded pdb=" OD2 ASP H 72 " pdb=" OG1 THR H 75 " model vdw 2.169 3.040 nonbonded pdb=" NH2 ARG L 50 " pdb=" OD1 ASN A 669 " model vdw 2.310 3.120 nonbonded pdb=" NH1 ARG L 54 " pdb=" OE1 GLU L 60 " model vdw 2.337 3.120 nonbonded pdb=" O ASN H 95 " pdb=" N GLY H 100D" model vdw 2.401 3.120 ... (remaining 20238 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.120 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 0.051 2578 Z= 0.181 Angle : 0.623 5.560 3486 Z= 0.330 Chirality : 0.044 0.208 381 Planarity : 0.004 0.021 438 Dihedral : 14.871 78.061 920 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.46), residues: 307 helix: 0.32 (0.62), residues: 67 sheet: -0.31 (0.58), residues: 87 loop : -1.65 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 105 TYR 0.011 0.002 TYR H 91 PHE 0.018 0.002 PHE A 660 TRP 0.017 0.002 TRP H 47 HIS 0.002 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 2576) covalent geometry : angle 0.62266 ( 3482) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.53519 ( 4) hydrogen bonds : bond 0.23340 ( 102) hydrogen bonds : angle 7.89094 ( 270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: L 22 THR cc_start: 0.7850 (t) cc_final: 0.7459 (p) REVERT: A 629 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7704 (mt-10) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0417 time to fit residues: 2.8189 Evaluate side-chains 52 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.160923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136572 restraints weight = 2960.703| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.21 r_work: 0.3387 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2578 Z= 0.205 Angle : 0.588 5.323 3486 Z= 0.318 Chirality : 0.044 0.136 381 Planarity : 0.004 0.023 438 Dihedral : 4.692 17.120 337 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.93 % Allowed : 9.16 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.45), residues: 307 helix: 0.67 (0.59), residues: 67 sheet: -0.90 (0.52), residues: 100 loop : -1.33 (0.47), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 50 TYR 0.010 0.001 TYR A 707 PHE 0.019 0.002 PHE A 660 TRP 0.016 0.002 TRP H 47 HIS 0.002 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 2576) covalent geometry : angle 0.58772 ( 3482) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.68715 ( 4) hydrogen bonds : bond 0.04291 ( 102) hydrogen bonds : angle 5.32072 ( 270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.058 Fit side-chains REVERT: H 17 SER cc_start: 0.8297 (m) cc_final: 0.8082 (p) REVERT: H 56 THR cc_start: 0.8859 (p) cc_final: 0.8623 (t) REVERT: H 73 GLU cc_start: 0.7020 (pm20) cc_final: 0.6644 (tm-30) REVERT: H 86 ASP cc_start: 0.8057 (t0) cc_final: 0.7513 (t0) REVERT: L 22 THR cc_start: 0.8010 (t) cc_final: 0.7648 (p) REVERT: A 678 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7708 (mtt) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 0.0360 time to fit residues: 2.8297 Evaluate side-chains 55 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 678 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.163001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.138146 restraints weight = 2954.203| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.25 r_work: 0.3394 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2578 Z= 0.144 Angle : 0.521 5.840 3486 Z= 0.277 Chirality : 0.041 0.134 381 Planarity : 0.003 0.022 438 Dihedral : 4.398 16.210 337 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.30 % Allowed : 12.09 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.45), residues: 307 helix: 1.03 (0.58), residues: 67 sheet: -0.81 (0.51), residues: 100 loop : -1.22 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.009 0.001 TYR A 707 PHE 0.013 0.001 PHE A 660 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2576) covalent geometry : angle 0.52084 ( 3482) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.46964 ( 4) hydrogen bonds : bond 0.03618 ( 102) hydrogen bonds : angle 4.81533 ( 270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.059 Fit side-chains REVERT: H 17 SER cc_start: 0.8279 (m) cc_final: 0.8024 (p) REVERT: H 73 GLU cc_start: 0.6934 (pm20) cc_final: 0.6453 (tt0) REVERT: H 86 ASP cc_start: 0.7593 (t0) cc_final: 0.7158 (t0) REVERT: A 581 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 678 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7700 (mtt) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.0391 time to fit residues: 2.8446 Evaluate side-chains 60 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain A residue 678 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27BASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.159810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136056 restraints weight = 2972.162| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.15 r_work: 0.3358 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2578 Z= 0.183 Angle : 0.578 8.493 3486 Z= 0.297 Chirality : 0.042 0.133 381 Planarity : 0.003 0.023 438 Dihedral : 4.405 16.469 337 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.76 % Allowed : 14.65 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.45), residues: 307 helix: 1.15 (0.56), residues: 67 sheet: -0.77 (0.51), residues: 100 loop : -1.21 (0.47), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 38 TYR 0.010 0.002 TYR A 707 PHE 0.010 0.002 PHE A 660 TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 2576) covalent geometry : angle 0.57767 ( 3482) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.47008 ( 4) hydrogen bonds : bond 0.03476 ( 102) hydrogen bonds : angle 4.71119 ( 270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.108 Fit side-chains REVERT: H 17 SER cc_start: 0.8485 (m) cc_final: 0.8127 (p) REVERT: H 62 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7634 (ptp-170) REVERT: H 86 ASP cc_start: 0.7804 (t0) cc_final: 0.7352 (t0) REVERT: L 105 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8896 (p) REVERT: A 581 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7886 (mt-10) REVERT: A 678 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7680 (mtt) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.0362 time to fit residues: 2.5370 Evaluate side-chains 60 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.158464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.134513 restraints weight = 2922.769| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.14 r_work: 0.3357 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2578 Z= 0.157 Angle : 0.551 7.670 3486 Z= 0.283 Chirality : 0.041 0.131 381 Planarity : 0.003 0.024 438 Dihedral : 4.306 15.719 337 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.66 % Allowed : 16.12 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.44), residues: 307 helix: 1.32 (0.57), residues: 67 sheet: -0.58 (0.55), residues: 87 loop : -1.33 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 94 TYR 0.009 0.001 TYR A 707 PHE 0.007 0.001 PHE A 660 TRP 0.009 0.001 TRP H 36 HIS 0.002 0.000 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 2576) covalent geometry : angle 0.55159 ( 3482) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.39352 ( 4) hydrogen bonds : bond 0.03282 ( 102) hydrogen bonds : angle 4.57113 ( 270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.096 Fit side-chains REVERT: H 17 SER cc_start: 0.8493 (m) cc_final: 0.8148 (p) REVERT: H 86 ASP cc_start: 0.7756 (t0) cc_final: 0.7241 (t0) REVERT: A 581 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 678 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7711 (mtt) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.0552 time to fit residues: 3.5692 Evaluate side-chains 57 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain A residue 678 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129413 restraints weight = 2966.795| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.12 r_work: 0.3304 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 2578 Z= 0.234 Angle : 0.626 6.734 3486 Z= 0.324 Chirality : 0.043 0.129 381 Planarity : 0.004 0.025 438 Dihedral : 4.566 16.692 337 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.66 % Allowed : 18.68 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.43), residues: 307 helix: 0.99 (0.57), residues: 67 sheet: -0.62 (0.56), residues: 82 loop : -1.29 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.011 0.002 TYR A 707 PHE 0.008 0.002 PHE A 662 TRP 0.011 0.002 TRP H 47 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 2576) covalent geometry : angle 0.62627 ( 3482) SS BOND : bond 0.00244 ( 2) SS BOND : angle 0.49435 ( 4) hydrogen bonds : bond 0.03632 ( 102) hydrogen bonds : angle 4.73209 ( 270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.091 Fit side-chains REVERT: H 17 SER cc_start: 0.8614 (m) cc_final: 0.8324 (p) REVERT: H 43 GLN cc_start: 0.7417 (mp10) cc_final: 0.7047 (mm-40) REVERT: H 63 PHE cc_start: 0.8717 (m-80) cc_final: 0.8513 (m-80) REVERT: H 86 ASP cc_start: 0.8166 (t0) cc_final: 0.7560 (t0) REVERT: A 581 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8100 (mt-10) REVERT: A 678 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7706 (mtt) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.0472 time to fit residues: 3.2412 Evaluate side-chains 57 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain A residue 678 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.156115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132713 restraints weight = 2939.344| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.09 r_work: 0.3342 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2578 Z= 0.160 Angle : 0.567 6.987 3486 Z= 0.290 Chirality : 0.041 0.130 381 Planarity : 0.003 0.025 438 Dihedral : 4.387 15.991 337 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.93 % Allowed : 20.51 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.43), residues: 307 helix: 1.24 (0.58), residues: 67 sheet: -0.45 (0.59), residues: 75 loop : -1.34 (0.41), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 62 TYR 0.010 0.002 TYR A 707 PHE 0.007 0.001 PHE A 662 TRP 0.012 0.001 TRP H 36 HIS 0.002 0.000 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 2576) covalent geometry : angle 0.56708 ( 3482) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.32602 ( 4) hydrogen bonds : bond 0.03169 ( 102) hydrogen bonds : angle 4.58866 ( 270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.097 Fit side-chains REVERT: H 17 SER cc_start: 0.8574 (m) cc_final: 0.8275 (p) REVERT: H 43 GLN cc_start: 0.7399 (mp10) cc_final: 0.7197 (mm-40) REVERT: H 86 ASP cc_start: 0.7846 (t0) cc_final: 0.7345 (t0) REVERT: A 581 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8056 (mt-10) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.0501 time to fit residues: 3.4900 Evaluate side-chains 56 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.157649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134486 restraints weight = 2943.032| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.08 r_work: 0.3366 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2578 Z= 0.131 Angle : 0.541 6.780 3486 Z= 0.276 Chirality : 0.040 0.129 381 Planarity : 0.003 0.026 438 Dihedral : 4.190 15.011 337 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.93 % Allowed : 20.15 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.44), residues: 307 helix: 1.49 (0.59), residues: 67 sheet: -0.38 (0.60), residues: 75 loop : -1.25 (0.41), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 62 TYR 0.009 0.002 TYR H 91 PHE 0.011 0.001 PHE H 63 TRP 0.010 0.001 TRP H 36 HIS 0.002 0.000 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2576) covalent geometry : angle 0.54171 ( 3482) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.23247 ( 4) hydrogen bonds : bond 0.02950 ( 102) hydrogen bonds : angle 4.42522 ( 270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.095 Fit side-chains REVERT: H 17 SER cc_start: 0.8563 (m) cc_final: 0.8217 (p) REVERT: H 86 ASP cc_start: 0.7704 (t0) cc_final: 0.7337 (t0) REVERT: A 581 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8042 (mt-10) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.0497 time to fit residues: 3.3348 Evaluate side-chains 55 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129887 restraints weight = 3009.120| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.11 r_work: 0.3301 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2578 Z= 0.204 Angle : 0.576 6.130 3486 Z= 0.302 Chirality : 0.042 0.128 381 Planarity : 0.004 0.027 438 Dihedral : 4.430 15.856 337 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.56 % Allowed : 20.51 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.44), residues: 307 helix: 1.22 (0.58), residues: 67 sheet: -0.49 (0.59), residues: 75 loop : -1.15 (0.42), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.010 0.002 TYR A 707 PHE 0.008 0.001 PHE H 63 TRP 0.010 0.002 TRP H 47 HIS 0.003 0.000 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 2576) covalent geometry : angle 0.57585 ( 3482) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.34368 ( 4) hydrogen bonds : bond 0.03339 ( 102) hydrogen bonds : angle 4.60707 ( 270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.121 Fit side-chains REVERT: H 17 SER cc_start: 0.8576 (m) cc_final: 0.8286 (p) REVERT: H 43 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7171 (mp10) REVERT: H 86 ASP cc_start: 0.7845 (t0) cc_final: 0.7419 (t0) REVERT: L 75 ILE cc_start: 0.7068 (mt) cc_final: 0.6779 (mt) REVERT: A 581 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 709 LYS cc_start: 0.8218 (mttm) cc_final: 0.7972 (mttm) outliers start: 7 outliers final: 7 residues processed: 54 average time/residue: 0.0596 time to fit residues: 3.9211 Evaluate side-chains 55 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.157679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135275 restraints weight = 3019.328| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.02 r_work: 0.3348 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2578 Z= 0.155 Angle : 0.560 7.192 3486 Z= 0.290 Chirality : 0.040 0.129 381 Planarity : 0.003 0.026 438 Dihedral : 4.346 15.593 337 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.56 % Allowed : 21.25 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.44), residues: 307 helix: 1.22 (0.59), residues: 69 sheet: -0.08 (0.62), residues: 69 loop : -1.31 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.010 0.002 TYR H 32 PHE 0.016 0.001 PHE H 63 TRP 0.010 0.001 TRP H 36 HIS 0.002 0.000 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2576) covalent geometry : angle 0.55976 ( 3482) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.26041 ( 4) hydrogen bonds : bond 0.03057 ( 102) hydrogen bonds : angle 4.53553 ( 270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.067 Fit side-chains REVERT: H 17 SER cc_start: 0.8563 (m) cc_final: 0.8252 (p) REVERT: H 43 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7250 (mp10) REVERT: H 86 ASP cc_start: 0.7793 (t0) cc_final: 0.7414 (t0) REVERT: A 581 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8057 (mt-10) outliers start: 7 outliers final: 7 residues processed: 58 average time/residue: 0.0467 time to fit residues: 3.2023 Evaluate side-chains 57 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 16 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.156320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133561 restraints weight = 2994.255| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.05 r_work: 0.3344 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2578 Z= 0.151 Angle : 0.559 9.094 3486 Z= 0.287 Chirality : 0.040 0.127 381 Planarity : 0.003 0.026 438 Dihedral : 4.326 15.266 337 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.93 % Allowed : 20.88 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.44), residues: 307 helix: 1.28 (0.59), residues: 69 sheet: -0.06 (0.62), residues: 69 loop : -1.28 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.012 0.002 TYR H 32 PHE 0.014 0.001 PHE H 63 TRP 0.011 0.001 TRP H 36 HIS 0.002 0.000 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 2576) covalent geometry : angle 0.55947 ( 3482) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.23581 ( 4) hydrogen bonds : bond 0.02962 ( 102) hydrogen bonds : angle 4.49971 ( 270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 702.20 seconds wall clock time: 12 minutes 39.48 seconds (759.48 seconds total)