Starting phenix.real_space_refine on Sat Jun 7 03:07:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fe1_50336/06_2025/9fe1_50336.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fe1_50336/06_2025/9fe1_50336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fe1_50336/06_2025/9fe1_50336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fe1_50336/06_2025/9fe1_50336.map" model { file = "/net/cci-nas-00/data/ceres_data/9fe1_50336/06_2025/9fe1_50336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fe1_50336/06_2025/9fe1_50336.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 13 5.16 5 C 2706 2.51 5 N 767 2.21 5 O 809 1.98 5 H 4163 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8458 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4325 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 262} Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1622 Classifications: {'peptide': 99} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 159 Classifications: {'peptide': 9} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 8} Chain: "D" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2352 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 4, 'TRANS': 152} Time building chain proxies: 4.54, per 1000 atoms: 0.54 Number of scatterers: 8458 At special positions: 0 Unit cell: (63.375, 68.25, 103.35, 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 13 16.00 O 809 8.00 N 767 7.00 C 2706 6.00 H 4163 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " 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: 2.04 Conformation dependent library (CDL) restraints added in 740.7 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 6 sheets defined 34.5% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 56 through 85 Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.553A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'D' and resid 14 through 25 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 92 through 103 Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 125 through 135 Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 158 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.706A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS A 114 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.173A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 214 through 218 removed outlier: 3.633A pdb=" N THR A 216 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 260 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN A 218 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A 258 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.504A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.504A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 228 hydrogen bonds defined for protein. 633 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: 2.70 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4163 1.03 - 1.23: 2 1.23 - 1.42: 1901 1.42 - 1.62: 2475 1.62 - 1.82: 20 Bond restraints: 8561 Sorted by residual: bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.30e+00 bond pdb=" N ASP D 13 " pdb=" CA ASP D 13 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" CG1 ILE D 95 " pdb=" CD1 ILE D 95 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.81e+00 bond pdb=" CD2 TYR A 113 " pdb=" CE2 TYR A 113 " ideal model delta sigma weight residual 1.382 1.335 0.047 3.00e-02 1.11e+03 2.46e+00 bond pdb=" N ASP D 13 " pdb=" H ASP D 13 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 8556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 14900 1.70 - 3.39: 481 3.39 - 5.09: 39 5.09 - 6.78: 3 6.78 - 8.48: 4 Bond angle restraints: 15427 Sorted by residual: angle pdb=" N GLY A 56 " pdb=" CA GLY A 56 " pdb=" C GLY A 56 " ideal model delta sigma weight residual 112.34 120.36 -8.02 2.04e+00 2.40e-01 1.55e+01 angle pdb=" CA ARG A 170 " pdb=" CB ARG A 170 " pdb=" CG ARG A 170 " ideal model delta sigma weight residual 114.10 106.64 7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB LYS D 17 " pdb=" CG LYS D 17 " pdb=" CD LYS D 17 " ideal model delta sigma weight residual 111.30 119.78 -8.48 2.30e+00 1.89e-01 1.36e+01 angle pdb=" CB ARG A 170 " pdb=" CG ARG A 170 " pdb=" CD ARG A 170 " ideal model delta sigma weight residual 111.30 119.06 -7.76 2.30e+00 1.89e-01 1.14e+01 angle pdb=" N LEU B 54 " pdb=" CA LEU B 54 " pdb=" C LEU B 54 " ideal model delta sigma weight residual 109.96 114.85 -4.89 1.49e+00 4.50e-01 1.08e+01 ... (remaining 15422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3623 17.40 - 34.80: 268 34.80 - 52.20: 73 52.20 - 69.60: 46 69.60 - 87.00: 15 Dihedral angle restraints: 4025 sinusoidal: 2151 harmonic: 1874 Sorted by residual: dihedral pdb=" CA PRO B 5 " pdb=" C PRO B 5 " pdb=" N LYS B 6 " pdb=" CA LYS B 6 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ILE B 35 " pdb=" C ILE B 35 " pdb=" N GLU B 36 " pdb=" CA GLU B 36 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ARG A 181 " pdb=" C ARG A 181 " pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 4022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 414 0.043 - 0.085: 166 0.085 - 0.127: 45 0.127 - 0.169: 11 0.169 - 0.212: 5 Chirality restraints: 641 Sorted by residual: chirality pdb=" CA ARG A 170 " pdb=" N ARG A 170 " pdb=" C ARG A 170 " pdb=" CB ARG A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO A 57 " pdb=" N PRO A 57 " pdb=" C PRO A 57 " pdb=" CB PRO A 57 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LYS A 68 " pdb=" N LYS A 68 " pdb=" C LYS A 68 " pdb=" CB LYS A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 638 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 52 " 0.011 2.00e-02 2.50e+03 3.17e-02 2.26e+01 pdb=" CG HIS D 52 " 0.005 2.00e-02 2.50e+03 pdb=" ND1 HIS D 52 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS D 52 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS D 52 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 HIS D 52 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 HIS D 52 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 HIS D 52 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 HIS D 52 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " 0.374 9.50e-02 1.11e+02 1.26e-01 2.19e+01 pdb=" NE ARG A 48 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 56 " -0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO A 57 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.057 5.00e-02 4.00e+02 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 396 2.15 - 2.76: 16140 2.76 - 3.37: 24385 3.37 - 3.99: 31696 3.99 - 4.60: 49229 Nonbonded interactions: 121846 Sorted by model distance: nonbonded pdb=" HH TYR A 159 " pdb=" O SER C 1 " model vdw 1.537 2.450 nonbonded pdb=" HG SER B 11 " pdb=" O HIS B 13 " model vdw 1.546 2.450 nonbonded pdb=" O ASP A 129 " pdb="HH11 ARG A 131 " model vdw 1.552 2.450 nonbonded pdb=" OE1 GLU D 127 " pdb=" H GLU D 127 " model vdw 1.557 2.450 nonbonded pdb=" O TRP A 60 " pdb=" HG1 THR A 64 " model vdw 1.560 2.450 ... (remaining 121841 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: 1.400 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: 0.140 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.480 Find NCS groups from input model: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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 : 0.005 0.065 4401 Z= 0.207 Angle : 0.835 8.481 5969 Z= 0.483 Chirality : 0.051 0.212 641 Planarity : 0.012 0.165 775 Dihedral : 15.082 87.003 1598 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.22 % Allowed : 2.23 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.32), residues: 531 helix: -1.80 (0.32), residues: 187 sheet: 0.85 (0.45), residues: 110 loop : -1.31 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP A 60 HIS 0.010 0.002 HIS A 260 PHE 0.020 0.003 PHE B 30 TYR 0.029 0.007 TYR A 171 ARG 0.039 0.005 ARG A 48 Details of bonding type rmsd hydrogen bonds : bond 0.19822 ( 213) hydrogen bonds : angle 7.75791 ( 633) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.24223 ( 6) covalent geometry : bond 0.00465 ( 4398) covalent geometry : angle 0.83420 ( 5963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.5906 time to fit residues: 69.8373 Evaluate side-chains 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN ** D 158 HIS ** 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 = 0.4143 r_free = 0.4143 target = 0.123293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.104182 restraints weight = 23021.916| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.68 r_work: 0.3725 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4401 Z= 0.190 Angle : 0.648 5.025 5969 Z= 0.352 Chirality : 0.042 0.147 641 Planarity : 0.005 0.061 775 Dihedral : 6.344 58.237 591 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 8.24 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.34), residues: 531 helix: 0.40 (0.35), residues: 181 sheet: 0.50 (0.41), residues: 120 loop : -0.29 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 60 HIS 0.006 0.002 HIS A 192 PHE 0.015 0.002 PHE A 9 TYR 0.019 0.003 TYR A 171 ARG 0.008 0.001 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 213) hydrogen bonds : angle 5.56544 ( 633) SS BOND : bond 0.00367 ( 3) SS BOND : angle 1.04825 ( 6) covalent geometry : bond 0.00423 ( 4398) covalent geometry : angle 0.64789 ( 5963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 60 average time/residue: 0.4664 time to fit residues: 33.9256 Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain C residue 9 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.122329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.103176 restraints weight = 23522.050| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.70 r_work: 0.3708 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.160 Angle : 0.585 4.975 5969 Z= 0.316 Chirality : 0.040 0.152 641 Planarity : 0.004 0.046 775 Dihedral : 5.875 55.363 591 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.00 % Allowed : 9.35 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.45 (0.34), residues: 531 helix: 1.02 (0.36), residues: 181 sheet: 0.29 (0.39), residues: 130 loop : -0.17 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 204 HIS 0.006 0.001 HIS A 260 PHE 0.011 0.001 PHE A 9 TYR 0.011 0.002 TYR A 113 ARG 0.004 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 213) hydrogen bonds : angle 5.00562 ( 633) SS BOND : bond 0.00729 ( 3) SS BOND : angle 1.10707 ( 6) covalent geometry : bond 0.00349 ( 4398) covalent geometry : angle 0.58443 ( 5963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8070 (mmtt) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.4543 time to fit residues: 31.9222 Evaluate side-chains 56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.121749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.102815 restraints weight = 23588.718| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.74 r_work: 0.3699 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4401 Z= 0.153 Angle : 0.559 5.215 5969 Z= 0.301 Chirality : 0.040 0.145 641 Planarity : 0.004 0.040 775 Dihedral : 5.703 53.363 591 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.00 % Allowed : 9.80 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.34), residues: 531 helix: 1.08 (0.36), residues: 181 sheet: 0.18 (0.40), residues: 130 loop : -0.18 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 51 HIS 0.005 0.001 HIS A 260 PHE 0.011 0.001 PHE A 9 TYR 0.011 0.002 TYR A 113 ARG 0.004 0.001 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 213) hydrogen bonds : angle 4.81475 ( 633) SS BOND : bond 0.00883 ( 3) SS BOND : angle 1.19523 ( 6) covalent geometry : bond 0.00337 ( 4398) covalent geometry : angle 0.55842 ( 5963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.4222 time to fit residues: 29.3736 Evaluate side-chains 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.0270 chunk 20 optimal weight: 0.0030 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5648 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.123450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104148 restraints weight = 23296.978| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.74 r_work: 0.3737 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4401 Z= 0.112 Angle : 0.519 5.219 5969 Z= 0.278 Chirality : 0.039 0.148 641 Planarity : 0.003 0.035 775 Dihedral : 5.384 52.472 591 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.45 % Allowed : 9.58 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.80 (0.35), residues: 531 helix: 1.44 (0.36), residues: 181 sheet: 0.10 (0.39), residues: 140 loop : 0.21 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 51 HIS 0.005 0.001 HIS A 260 PHE 0.008 0.001 PHE A 9 TYR 0.010 0.001 TYR A 99 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 213) hydrogen bonds : angle 4.57307 ( 633) SS BOND : bond 0.00694 ( 3) SS BOND : angle 1.20650 ( 6) covalent geometry : bond 0.00243 ( 4398) covalent geometry : angle 0.51805 ( 5963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7504 (t0) cc_final: 0.7288 (t0) REVERT: B 6 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7953 (tptt) outliers start: 11 outliers final: 10 residues processed: 60 average time/residue: 0.4149 time to fit residues: 30.8543 Evaluate side-chains 58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.121359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.102726 restraints weight = 23651.232| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.75 r_work: 0.3703 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.141 Angle : 0.537 5.222 5969 Z= 0.287 Chirality : 0.039 0.143 641 Planarity : 0.003 0.034 775 Dihedral : 5.436 48.249 591 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.67 % Allowed : 9.80 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.74 (0.35), residues: 531 helix: 1.36 (0.36), residues: 181 sheet: 0.02 (0.40), residues: 133 loop : 0.23 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 51 HIS 0.006 0.001 HIS A 188 PHE 0.009 0.001 PHE A 9 TYR 0.011 0.002 TYR A 116 ARG 0.004 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 213) hydrogen bonds : angle 4.53558 ( 633) SS BOND : bond 0.00679 ( 3) SS BOND : angle 1.00595 ( 6) covalent geometry : bond 0.00310 ( 4398) covalent geometry : angle 0.53608 ( 5963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7547 (t0) cc_final: 0.7334 (t0) REVERT: B 6 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7971 (tptt) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.4017 time to fit residues: 29.7734 Evaluate side-chains 56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.120585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.101580 restraints weight = 23876.016| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.72 r_work: 0.3689 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4401 Z= 0.161 Angle : 0.557 5.132 5969 Z= 0.299 Chirality : 0.039 0.137 641 Planarity : 0.004 0.035 775 Dihedral : 5.475 48.722 591 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.67 % Allowed : 11.58 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.46 (0.35), residues: 531 helix: 1.12 (0.36), residues: 181 sheet: -0.40 (0.40), residues: 137 loop : 0.30 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 51 HIS 0.005 0.001 HIS A 188 PHE 0.009 0.001 PHE A 9 TYR 0.011 0.002 TYR A 99 ARG 0.004 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 213) hydrogen bonds : angle 4.57171 ( 633) SS BOND : bond 0.00693 ( 3) SS BOND : angle 1.15186 ( 6) covalent geometry : bond 0.00355 ( 4398) covalent geometry : angle 0.55610 ( 5963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7959 (mmtm) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.3957 time to fit residues: 28.2994 Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 0.0470 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.3082 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.119765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.100832 restraints weight = 24126.652| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.72 r_work: 0.3677 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4401 Z= 0.175 Angle : 0.572 5.194 5969 Z= 0.308 Chirality : 0.040 0.136 641 Planarity : 0.004 0.034 775 Dihedral : 5.504 49.364 591 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.67 % Allowed : 11.58 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.18 (0.35), residues: 531 helix: 0.91 (0.36), residues: 181 sheet: -0.51 (0.39), residues: 146 loop : 0.12 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 51 HIS 0.005 0.001 HIS A 188 PHE 0.009 0.002 PHE A 9 TYR 0.011 0.002 TYR A 99 ARG 0.004 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 213) hydrogen bonds : angle 4.62909 ( 633) SS BOND : bond 0.00635 ( 3) SS BOND : angle 1.05372 ( 6) covalent geometry : bond 0.00386 ( 4398) covalent geometry : angle 0.57116 ( 5963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7955 (mmtm) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.4412 time to fit residues: 29.9185 Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 36 optimal weight: 0.4980 chunk 46 optimal weight: 0.0370 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.121830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.102878 restraints weight = 23892.696| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.73 r_work: 0.3718 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.114 Angle : 0.531 5.306 5969 Z= 0.283 Chirality : 0.038 0.140 641 Planarity : 0.003 0.035 775 Dihedral : 5.174 42.583 591 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.00 % Allowed : 12.03 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.36), residues: 531 helix: 1.34 (0.36), residues: 181 sheet: -0.37 (0.40), residues: 146 loop : 0.22 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 51 HIS 0.004 0.001 HIS A 188 PHE 0.007 0.001 PHE A 9 TYR 0.012 0.001 TYR A 99 ARG 0.006 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 213) hydrogen bonds : angle 4.42910 ( 633) SS BOND : bond 0.00585 ( 3) SS BOND : angle 1.04471 ( 6) covalent geometry : bond 0.00250 ( 4398) covalent geometry : angle 0.53025 ( 5963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7902 (mmtm) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.5157 time to fit residues: 35.1982 Evaluate side-chains 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.122253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.103520 restraints weight = 23990.552| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.75 r_work: 0.3710 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.123 Angle : 0.538 5.267 5969 Z= 0.287 Chirality : 0.038 0.137 641 Planarity : 0.003 0.033 775 Dihedral : 5.107 43.648 591 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.78 % Allowed : 13.59 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.36), residues: 531 helix: 1.40 (0.36), residues: 181 sheet: -0.36 (0.41), residues: 146 loop : 0.19 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 51 HIS 0.004 0.001 HIS A 188 PHE 0.007 0.001 PHE A 9 TYR 0.011 0.001 TYR A 99 ARG 0.005 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 213) hydrogen bonds : angle 4.41354 ( 633) SS BOND : bond 0.00590 ( 3) SS BOND : angle 1.02433 ( 6) covalent geometry : bond 0.00272 ( 4398) covalent geometry : angle 0.53703 ( 5963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7855 (mmtm) outliers start: 8 outliers final: 8 residues processed: 52 average time/residue: 0.4665 time to fit residues: 29.8839 Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.121057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.102498 restraints weight = 24543.749| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.70 r_work: 0.3694 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4401 Z= 0.149 Angle : 0.555 5.183 5969 Z= 0.298 Chirality : 0.039 0.137 641 Planarity : 0.004 0.033 775 Dihedral : 5.263 48.720 591 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.00 % Allowed : 13.59 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.28 (0.36), residues: 531 helix: 1.20 (0.36), residues: 181 sheet: -0.66 (0.40), residues: 152 loop : 0.15 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 51 HIS 0.005 0.001 HIS A 188 PHE 0.008 0.001 PHE A 9 TYR 0.012 0.002 TYR A 99 ARG 0.006 0.000 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 213) hydrogen bonds : angle 4.49412 ( 633) SS BOND : bond 0.00570 ( 3) SS BOND : angle 0.93255 ( 6) covalent geometry : bond 0.00330 ( 4398) covalent geometry : angle 0.55451 ( 5963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6037.09 seconds wall clock time: 104 minutes 15.98 seconds (6255.98 seconds total)