Starting phenix.real_space_refine on Fri Jul 25 02:15:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m8j_23717/07_2025/7m8j_23717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m8j_23717/07_2025/7m8j_23717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m8j_23717/07_2025/7m8j_23717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m8j_23717/07_2025/7m8j_23717.map" model { file = "/net/cci-nas-00/data/ceres_data/7m8j_23717/07_2025/7m8j_23717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m8j_23717/07_2025/7m8j_23717.cif" } resolution = 3.48 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= -0.008 sd= 0.083 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2238 2.51 5 N 589 2.21 5 O 676 1.98 5 H 3398 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6915 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3541 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Chain: "H" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1799 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1575 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Time building chain proxies: 4.98, per 1000 atoms: 0.72 Number of scatterers: 6915 At special positions: 0 Unit cell: (100.1, 74.8, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 676 8.00 N 589 7.00 C 2238 6.00 H 3398 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 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: 1.76 Conformation dependent library (CDL) restraints added in 668.1 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 3.1% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.232A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.013A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.985A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.247A pdb=" N GLU H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET H 39 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.020A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.020A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.025A pdb=" N VAL L 19 " --> pdb=" O ILE L 91 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 91 " --> pdb=" O VAL L 19 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 3398 1.04 - 1.26: 569 1.26 - 1.47: 1552 1.47 - 1.69: 1466 1.69 - 1.91: 20 Bond restraints: 7005 Sorted by residual: bond pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 1.808 1.906 -0.098 3.30e-02 9.18e+02 8.80e+00 bond pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " ideal model delta sigma weight residual 1.808 1.718 0.090 3.30e-02 9.18e+02 7.51e+00 bond pdb=" CG GLN H 72 " pdb=" CD GLN H 72 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.97e+00 bond pdb=" CB ASP A 111 " pdb=" CG ASP A 111 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" N GLN H 72 " pdb=" CA GLN H 72 " ideal model delta sigma weight residual 1.458 1.475 -0.017 1.23e-02 6.61e+03 1.84e+00 ... (remaining 7000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 12031 1.70 - 3.40: 501 3.40 - 5.09: 47 5.09 - 6.79: 11 6.79 - 8.49: 2 Bond angle restraints: 12592 Sorted by residual: angle pdb=" N PHE H 71 " pdb=" CA PHE H 71 " pdb=" C PHE H 71 " ideal model delta sigma weight residual 113.28 119.15 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N CYS A 131 " pdb=" CA CYS A 131 " pdb=" C CYS A 131 " ideal model delta sigma weight residual 109.07 102.45 6.62 1.52e+00 4.33e-01 1.90e+01 angle pdb=" N THR A 167 " pdb=" CA THR A 167 " pdb=" C THR A 167 " ideal model delta sigma weight residual 110.80 118.99 -8.19 2.13e+00 2.20e-01 1.48e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 122.89 -8.49 2.30e+00 1.89e-01 1.36e+01 angle pdb=" N LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " ideal model delta sigma weight residual 110.39 116.08 -5.69 1.75e+00 3.27e-01 1.06e+01 ... (remaining 12587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3013 17.94 - 35.88: 250 35.88 - 53.81: 68 53.81 - 71.75: 21 71.75 - 89.69: 3 Dihedral angle restraints: 3355 sinusoidal: 1778 harmonic: 1577 Sorted by residual: dihedral pdb=" CA LYS A 97 " pdb=" C LYS A 97 " pdb=" N SER A 98 " pdb=" CA SER A 98 " ideal model delta harmonic sigma weight residual 180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PHE H 71 " pdb=" C PHE H 71 " pdb=" N GLN H 72 " pdb=" CA GLN H 72 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PRO A 217 " pdb=" C PRO A 217 " pdb=" N GLN A 218 " pdb=" CA GLN A 218 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 3352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 341 0.044 - 0.088: 131 0.088 - 0.131: 53 0.131 - 0.175: 10 0.175 - 0.219: 3 Chirality restraints: 538 Sorted by residual: chirality pdb=" CG LEU A 249 " pdb=" CB LEU A 249 " pdb=" CD1 LEU A 249 " pdb=" CD2 LEU A 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA CYS A 131 " pdb=" N CYS A 131 " pdb=" C CYS A 131 " pdb=" CB CYS A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LYS A 113 " pdb=" N LYS A 113 " pdb=" C LYS A 113 " pdb=" CB LYS A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 535 not shown) Planarity restraints: 1053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 95 " 0.033 9.50e-02 1.11e+02 3.47e-02 2.44e+01 pdb=" NE ARG H 95 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG H 95 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG H 95 " -0.076 2.00e-02 2.50e+03 pdb=" NH2 ARG H 95 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG H 95 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG H 95 " 0.058 2.00e-02 2.50e+03 pdb="HH21 ARG H 95 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG H 95 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 69 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLN H 69 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN H 69 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS H 70 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 75 " 0.005 9.50e-02 1.11e+02 2.28e-02 1.16e+01 pdb=" NE ARG H 75 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG H 75 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 75 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG H 75 " -0.045 2.00e-02 2.50e+03 pdb="HH11 ARG H 75 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG H 75 " -0.013 2.00e-02 2.50e+03 pdb="HH21 ARG H 75 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 75 " 0.044 2.00e-02 2.50e+03 ... (remaining 1050 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 171 2.10 - 2.73: 11573 2.73 - 3.35: 17850 3.35 - 3.98: 22465 3.98 - 4.60: 35263 Nonbonded interactions: 87322 Sorted by model distance: nonbonded pdb=" OD2 ASP A 111 " pdb=" HZ1 LYS A 113 " model vdw 1.481 2.450 nonbonded pdb=" O ARG A 21 " pdb="HE22 GLN A 23 " model vdw 1.488 2.450 nonbonded pdb=" OD2 ASP A 111 " pdb=" HZ3 LYS A 113 " model vdw 1.573 2.450 nonbonded pdb=" O PRO L 15 " pdb="HE22 GLN L 17 " model vdw 1.659 2.450 nonbonded pdb=" OE1 GLN H 72 " pdb=" H GLN H 72 " model vdw 1.701 2.450 ... (remaining 87317 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: 4.680 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: 0.130 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.510 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.006 0.098 3611 Z= 0.264 Angle : 0.977 10.056 4914 Z= 0.545 Chirality : 0.055 0.219 538 Planarity : 0.005 0.037 627 Dihedral : 14.719 89.686 1268 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.37), residues: 443 helix: None (None), residues: 0 sheet: 1.25 (0.38), residues: 172 loop : -1.30 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP L 41 HIS 0.013 0.003 HIS L 115 PHE 0.016 0.003 PHE L 118 TYR 0.021 0.004 TYR H 28 ARG 0.045 0.008 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.25260 ( 115) hydrogen bonds : angle 8.71538 ( 282) SS BOND : bond 0.00791 ( 4) SS BOND : angle 4.60506 ( 8) covalent geometry : bond 0.00627 ( 3607) covalent geometry : angle 0.96043 ( 4906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.541 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2714 time to fit residues: 14.8400 Evaluate side-chains 34 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 185 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080389 restraints weight = 20979.605| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.56 r_work: 0.3076 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3611 Z= 0.165 Angle : 0.691 4.951 4914 Z= 0.379 Chirality : 0.046 0.147 538 Planarity : 0.004 0.026 627 Dihedral : 6.522 23.016 485 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.03 % Allowed : 7.24 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 1.02 (0.39), residues: 171 loop : -1.08 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.008 0.002 HIS L 115 PHE 0.011 0.001 PHE A 92 TYR 0.011 0.002 TYR A 266 ARG 0.007 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.06004 ( 115) hydrogen bonds : angle 6.59300 ( 282) SS BOND : bond 0.00479 ( 4) SS BOND : angle 1.82721 ( 8) covalent geometry : bond 0.00384 ( 3607) covalent geometry : angle 0.68777 ( 4906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.702 Fit side-chains REVERT: A 137 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7996 (t0) REVERT: H 11 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7693 (mt-10) REVERT: H 90 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7120 (tm-30) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.3101 time to fit residues: 16.7455 Evaluate side-chains 38 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** 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 = 0.3737 r_free = 0.3737 target = 0.111526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080984 restraints weight = 21303.991| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.50 r_work: 0.3093 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3611 Z= 0.152 Angle : 0.609 5.352 4914 Z= 0.331 Chirality : 0.044 0.143 538 Planarity : 0.003 0.024 627 Dihedral : 6.054 21.544 485 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.78 % Allowed : 9.56 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.84 (0.39), residues: 171 loop : -1.11 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.006 0.001 HIS L 115 PHE 0.009 0.001 PHE A 86 TYR 0.011 0.001 TYR A 266 ARG 0.003 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 115) hydrogen bonds : angle 6.14207 ( 282) SS BOND : bond 0.00477 ( 4) SS BOND : angle 1.47754 ( 8) covalent geometry : bond 0.00358 ( 3607) covalent geometry : angle 0.60646 ( 4906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.539 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.2709 time to fit residues: 14.5375 Evaluate side-chains 35 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.0570 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.0000 chunk 40 optimal weight: 0.3980 overall best weight: 0.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** H 6 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 = 0.3747 r_free = 0.3747 target = 0.112292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081583 restraints weight = 21099.537| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.50 r_work: 0.3105 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3611 Z= 0.116 Angle : 0.562 5.282 4914 Z= 0.303 Chirality : 0.044 0.140 538 Planarity : 0.003 0.023 627 Dihedral : 5.548 19.504 485 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.78 % Allowed : 13.18 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 0.95 (0.39), residues: 167 loop : -1.13 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.007 0.001 PHE A 92 TYR 0.008 0.001 TYR A 266 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 115) hydrogen bonds : angle 5.79364 ( 282) SS BOND : bond 0.00397 ( 4) SS BOND : angle 1.14950 ( 8) covalent geometry : bond 0.00275 ( 3607) covalent geometry : angle 0.56086 ( 4906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.868 Fit side-chains REVERT: A 96 GLU cc_start: 0.8739 (tp30) cc_final: 0.8488 (tp30) REVERT: L 17 GLN cc_start: 0.8139 (mp10) cc_final: 0.7938 (mp10) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.3345 time to fit residues: 19.1405 Evaluate side-chains 38 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** 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 = 0.3743 r_free = 0.3743 target = 0.111835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081172 restraints weight = 20947.660| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.49 r_work: 0.3100 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3611 Z= 0.135 Angle : 0.555 5.214 4914 Z= 0.296 Chirality : 0.043 0.140 538 Planarity : 0.003 0.027 627 Dihedral : 5.356 18.795 485 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.52 % Allowed : 14.99 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.91 (0.38), residues: 167 loop : -1.18 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 41 HIS 0.006 0.001 HIS L 115 PHE 0.009 0.001 PHE A 86 TYR 0.010 0.001 TYR A 266 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 115) hydrogen bonds : angle 5.66150 ( 282) SS BOND : bond 0.00506 ( 4) SS BOND : angle 1.17182 ( 8) covalent geometry : bond 0.00327 ( 3607) covalent geometry : angle 0.55295 ( 4906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8780 (tp30) cc_final: 0.8443 (tp30) outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.3717 time to fit residues: 19.4030 Evaluate side-chains 37 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** 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 = 0.3715 r_free = 0.3715 target = 0.110898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079205 restraints weight = 21132.220| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.59 r_work: 0.3048 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3611 Z= 0.144 Angle : 0.553 5.120 4914 Z= 0.295 Chirality : 0.043 0.142 538 Planarity : 0.003 0.029 627 Dihedral : 5.169 18.094 485 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.29 % Allowed : 14.73 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 1.01 (0.38), residues: 162 loop : -1.34 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.006 0.001 HIS L 115 PHE 0.011 0.001 PHE A 86 TYR 0.012 0.001 TYR A 266 ARG 0.005 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 115) hydrogen bonds : angle 5.54789 ( 282) SS BOND : bond 0.00403 ( 4) SS BOND : angle 1.07973 ( 8) covalent geometry : bond 0.00348 ( 3607) covalent geometry : angle 0.55174 ( 4906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8912 (tp30) cc_final: 0.8546 (tp30) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.4973 time to fit residues: 27.2511 Evaluate side-chains 40 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** 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 = 0.3705 r_free = 0.3705 target = 0.110254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078451 restraints weight = 20924.875| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.58 r_work: 0.3038 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3611 Z= 0.170 Angle : 0.566 5.156 4914 Z= 0.304 Chirality : 0.043 0.145 538 Planarity : 0.003 0.032 627 Dihedral : 5.183 18.836 485 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.07 % Allowed : 15.25 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.80 (0.38), residues: 175 loop : -1.32 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.013 0.001 PHE A 86 TYR 0.011 0.001 TYR H 103 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 115) hydrogen bonds : angle 5.57340 ( 282) SS BOND : bond 0.00451 ( 4) SS BOND : angle 1.14818 ( 8) covalent geometry : bond 0.00411 ( 3607) covalent geometry : angle 0.56461 ( 4906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7542 (mttp) REVERT: H 97 GLU cc_start: 0.8598 (mp0) cc_final: 0.7981 (pp20) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.3259 time to fit residues: 17.5608 Evaluate side-chains 44 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.0060 chunk 34 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** 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 = 0.3719 r_free = 0.3719 target = 0.110939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079341 restraints weight = 21240.626| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.61 r_work: 0.3060 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3611 Z= 0.117 Angle : 0.534 5.023 4914 Z= 0.285 Chirality : 0.043 0.139 538 Planarity : 0.003 0.029 627 Dihedral : 4.993 19.115 485 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.81 % Allowed : 16.54 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 0.87 (0.37), residues: 181 loop : -1.36 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.004 0.001 HIS L 115 PHE 0.008 0.001 PHE A 92 TYR 0.008 0.001 TYR H 103 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 115) hydrogen bonds : angle 5.41263 ( 282) SS BOND : bond 0.00399 ( 4) SS BOND : angle 0.94968 ( 8) covalent geometry : bond 0.00277 ( 3607) covalent geometry : angle 0.53266 ( 4906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8868 (tp30) cc_final: 0.8529 (tp30) REVERT: A 185 ASN cc_start: 0.7262 (OUTLIER) cc_final: 0.6073 (t0) REVERT: A 187 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7583 (mttp) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.2860 time to fit residues: 16.5796 Evaluate side-chains 45 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** 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 = 0.3713 r_free = 0.3713 target = 0.110674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.078841 restraints weight = 21278.271| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.61 r_work: 0.3045 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3611 Z= 0.145 Angle : 0.554 6.015 4914 Z= 0.294 Chirality : 0.043 0.143 538 Planarity : 0.003 0.028 627 Dihedral : 5.011 19.631 485 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.33 % Allowed : 16.80 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.85 (0.38), residues: 181 loop : -1.40 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 41 HIS 0.005 0.001 HIS L 115 PHE 0.010 0.001 PHE A 86 TYR 0.010 0.001 TYR A 266 ARG 0.004 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 115) hydrogen bonds : angle 5.44031 ( 282) SS BOND : bond 0.00554 ( 4) SS BOND : angle 1.18139 ( 8) covalent geometry : bond 0.00352 ( 3607) covalent geometry : angle 0.55244 ( 4906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8866 (tp30) cc_final: 0.8541 (tp30) REVERT: A 185 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.6104 (t0) REVERT: A 187 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7663 (mttp) REVERT: H 97 GLU cc_start: 0.8750 (mp0) cc_final: 0.8286 (pp20) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 0.3703 time to fit residues: 21.3952 Evaluate side-chains 46 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** 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 = 0.3707 r_free = 0.3707 target = 0.110364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078410 restraints weight = 21600.228| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.63 r_work: 0.3033 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3611 Z= 0.165 Angle : 0.567 6.066 4914 Z= 0.303 Chirality : 0.043 0.145 538 Planarity : 0.003 0.028 627 Dihedral : 5.062 20.630 485 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.07 % Allowed : 17.31 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.84 (0.37), residues: 183 loop : -1.46 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.011 0.001 PHE A 86 TYR 0.011 0.001 TYR H 103 ARG 0.004 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 115) hydrogen bonds : angle 5.45421 ( 282) SS BOND : bond 0.00467 ( 4) SS BOND : angle 1.13916 ( 8) covalent geometry : bond 0.00402 ( 3607) covalent geometry : angle 0.56527 ( 4906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8863 (tp30) cc_final: 0.8532 (tp30) REVERT: A 185 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.6154 (t0) REVERT: A 187 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7643 (mttp) REVERT: H 90 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7175 (tm-30) REVERT: H 97 GLU cc_start: 0.8594 (mp0) cc_final: 0.8101 (pp20) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.4326 time to fit residues: 25.6876 Evaluate side-chains 47 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** 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 = 0.3726 r_free = 0.3726 target = 0.111405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079724 restraints weight = 21290.025| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.62 r_work: 0.3065 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3611 Z= 0.112 Angle : 0.533 5.339 4914 Z= 0.282 Chirality : 0.043 0.137 538 Planarity : 0.003 0.025 627 Dihedral : 4.878 19.984 485 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.81 % Allowed : 18.09 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 0.90 (0.38), residues: 183 loop : -1.46 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.004 0.001 HIS L 115 PHE 0.007 0.001 PHE A 86 TYR 0.008 0.001 TYR A 266 ARG 0.004 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 115) hydrogen bonds : angle 5.33429 ( 282) SS BOND : bond 0.00420 ( 4) SS BOND : angle 0.99721 ( 8) covalent geometry : bond 0.00269 ( 3607) covalent geometry : angle 0.53171 ( 4906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5340.61 seconds wall clock time: 97 minutes 25.00 seconds (5845.00 seconds total)