Starting phenix.real_space_refine on Fri Aug 22 14:03:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o60_70155/08_2025/9o60_70155.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o60_70155/08_2025/9o60_70155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o60_70155/08_2025/9o60_70155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o60_70155/08_2025/9o60_70155.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o60_70155/08_2025/9o60_70155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o60_70155/08_2025/9o60_70155.map" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2345 2.51 5 N 604 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3627 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 441 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain breaks: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "a" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1495 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "b" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1691 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain breaks: 2 Time building chain proxies: 1.23, per 1000 atoms: 0.34 Number of scatterers: 3627 At special positions: 0 Unit cell: (77.08, 69.7, 82.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 664 8.00 N 604 7.00 C 2345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 91 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 135.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 12 sheets defined 3.8% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'a' and resid 82 through 86 removed outlier: 3.525A pdb=" N ASP a 85 " --> pdb=" O GLN a 82 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER a 86 " --> pdb=" O LEU a 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 82 through 86' Processing helix chain 'b' and resid 86 through 90 Processing helix chain 'b' and resid 133 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 7.331A pdb=" N SER A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.850A pdb=" N LEU A 48 " --> pdb=" O TRP A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'a' and resid 11 through 14 removed outlier: 6.592A pdb=" N ILE a 34 " --> pdb=" O ARG a 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG a 50 " --> pdb=" O ILE a 34 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP a 36 " --> pdb=" O LEU a 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 11 through 14 Processing sheet with id=AA6, first strand: chain 'a' and resid 19 through 21 removed outlier: 3.694A pdb=" N ALA a 75 " --> pdb=" O ASN a 66 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR a 63 " --> pdb=" O SER a 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 137 through 140 removed outlier: 3.826A pdb=" N LYS a 181 " --> pdb=" O SER a 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 10 through 14 removed outlier: 5.109A pdb=" N TRP b 98 " --> pdb=" O TYR b 32 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR b 32 " --> pdb=" O TRP b 98 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE b 33 " --> pdb=" O TYR b 49 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR b 49 " --> pdb=" O ILE b 33 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TRP b 35 " --> pdb=" O LEU b 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 10 through 14 Processing sheet with id=AB1, first strand: chain 'b' and resid 19 through 22 Processing sheet with id=AB2, first strand: chain 'b' and resid 125 through 129 removed outlier: 3.503A pdb=" N LEU b 145 " --> pdb=" O PHE b 129 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR b 183 " --> pdb=" O LYS b 150 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE b 186 " --> pdb=" O ASN b 175 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASN b 175 " --> pdb=" O PHE b 186 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TRP b 188 " --> pdb=" O GLU b 173 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU b 173 " --> pdb=" O TRP b 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 157 through 161 133 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1106 1.34 - 1.46: 919 1.46 - 1.58: 1677 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3722 Sorted by residual: bond pdb=" N LEU b 147 " pdb=" CA LEU b 147 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.18e-02 7.18e+03 7.09e+00 bond pdb=" N LEU b 145 " pdb=" CA LEU b 145 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.21e-02 6.83e+03 4.45e+00 bond pdb=" N CYS b 146 " pdb=" CA CYS b 146 " ideal model delta sigma weight residual 1.456 1.480 -0.023 1.21e-02 6.83e+03 3.65e+00 bond pdb=" N LEU b 148 " pdb=" CA LEU b 148 " ideal model delta sigma weight residual 1.458 1.478 -0.020 1.19e-02 7.06e+03 2.87e+00 bond pdb=" CG LEU b 48 " pdb=" CD2 LEU b 48 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 ... (remaining 3717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4719 1.21 - 2.42: 261 2.42 - 3.63: 54 3.63 - 4.84: 6 4.84 - 6.04: 6 Bond angle restraints: 5046 Sorted by residual: angle pdb=" N LEU b 147 " pdb=" CA LEU b 147 " pdb=" CB LEU b 147 " ideal model delta sigma weight residual 110.85 115.75 -4.90 1.54e+00 4.22e-01 1.01e+01 angle pdb=" CA TRP a 109 " pdb=" CB TRP a 109 " pdb=" CG TRP a 109 " ideal model delta sigma weight residual 113.60 119.54 -5.94 1.90e+00 2.77e-01 9.79e+00 angle pdb=" C SER a 108 " pdb=" N TRP a 109 " pdb=" CA TRP a 109 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.83e+00 angle pdb=" N ILE b 133 " pdb=" CA ILE b 133 " pdb=" C ILE b 133 " ideal model delta sigma weight residual 112.98 109.57 3.41 1.25e+00 6.40e-01 7.46e+00 angle pdb=" C CYS b 146 " pdb=" N LEU b 147 " pdb=" CA LEU b 147 " ideal model delta sigma weight residual 122.92 118.33 4.59 1.76e+00 3.23e-01 6.81e+00 ... (remaining 5041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1894 17.95 - 35.90: 222 35.90 - 53.85: 69 53.85 - 71.80: 14 71.80 - 89.75: 5 Dihedral angle restraints: 2204 sinusoidal: 882 harmonic: 1322 Sorted by residual: dihedral pdb=" CB CYS a 23 " pdb=" SG CYS a 23 " pdb=" SG CYS a 91 " pdb=" CB CYS a 91 " ideal model delta sinusoidal sigma weight residual 93.00 41.88 51.12 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CB CYS b 23 " pdb=" SG CYS b 23 " pdb=" SG CYS b 95 " pdb=" CB CYS b 95 " ideal model delta sinusoidal sigma weight residual 93.00 138.69 -45.69 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CA LEU b 48 " pdb=" C LEU b 48 " pdb=" N TYR b 49 " pdb=" CA TYR b 49 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 2201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 431 0.052 - 0.104: 95 0.104 - 0.157: 25 0.157 - 0.209: 2 0.209 - 0.261: 1 Chirality restraints: 554 Sorted by residual: chirality pdb=" CG LEU b 147 " pdb=" CB LEU b 147 " pdb=" CD1 LEU b 147 " pdb=" CD2 LEU b 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL a 74 " pdb=" CA VAL a 74 " pdb=" CG1 VAL a 74 " pdb=" CG2 VAL a 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA CYS b 146 " pdb=" N CYS b 146 " pdb=" C CYS b 146 " pdb=" CB CYS b 146 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 551 not shown) Planarity restraints: 620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO a 96 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C PRO a 96 " 0.036 2.00e-02 2.50e+03 pdb=" O PRO a 96 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS a 97 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 76 " 0.012 2.00e-02 2.50e+03 1.20e-02 3.58e+00 pdb=" CG TRP b 76 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP b 76 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP b 76 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP b 76 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP b 76 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP b 76 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 76 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 76 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP b 76 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET a 13 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO a 14 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO a 14 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO a 14 " 0.021 5.00e-02 4.00e+02 ... (remaining 617 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 282 2.74 - 3.28: 3362 3.28 - 3.82: 6260 3.82 - 4.36: 7534 4.36 - 4.90: 12699 Nonbonded interactions: 30137 Sorted by model distance: nonbonded pdb=" NE2 HIS a 97 " pdb=" O ARG b 100 " model vdw 2.197 3.120 nonbonded pdb=" NE2 HIS b 159 " pdb=" OE1 GLN b 161 " model vdw 2.245 3.120 nonbonded pdb=" O ASP a 85 " pdb=" OH TYR a 89 " model vdw 2.248 3.040 nonbonded pdb=" O THR A 72 " pdb=" OG1 THR A 72 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP b 99 " pdb=" N ARG b 100 " model vdw 2.264 3.120 ... (remaining 30132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 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 0.050 3724 Z= 0.220 Angle : 0.666 6.045 5050 Z= 0.368 Chirality : 0.049 0.261 554 Planarity : 0.005 0.039 620 Dihedral : 17.461 89.751 1340 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.24 % Favored : 91.53 % Rotamer: Outliers : 0.75 % Allowed : 25.56 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.39), residues: 425 helix: -4.44 (0.66), residues: 6 sheet: -0.32 (0.36), residues: 209 loop : -2.35 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG b 75 TYR 0.021 0.002 TYR b 36 PHE 0.009 0.002 PHE a 90 TRP 0.031 0.002 TRP b 76 HIS 0.003 0.001 HIS a 202 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 3722) covalent geometry : angle 0.66557 ( 5046) SS BOND : bond 0.00306 ( 2) SS BOND : angle 1.31747 ( 4) hydrogen bonds : bond 0.10680 ( 119) hydrogen bonds : angle 7.62215 ( 312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: b 82 LEU cc_start: 0.7478 (mp) cc_final: 0.7268 (mp) outliers start: 3 outliers final: 1 residues processed: 103 average time/residue: 0.4848 time to fit residues: 51.5685 Evaluate side-chains 75 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 146 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 129 GLN b 29 ASN b 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.167585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.136395 restraints weight = 5661.316| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.86 r_work: 0.3976 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3724 Z= 0.161 Angle : 0.648 9.424 5050 Z= 0.327 Chirality : 0.046 0.195 554 Planarity : 0.005 0.045 620 Dihedral : 4.680 26.562 482 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.29 % Favored : 92.47 % Rotamer: Outliers : 5.01 % Allowed : 25.31 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.39), residues: 425 helix: -3.94 (1.05), residues: 7 sheet: -0.29 (0.35), residues: 209 loop : -2.22 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 74 TYR 0.012 0.002 TYR b 69 PHE 0.007 0.001 PHE b 151 TRP 0.015 0.001 TRP a 109 HIS 0.003 0.001 HIS b 159 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3722) covalent geometry : angle 0.64779 ( 5046) SS BOND : bond 0.00345 ( 2) SS BOND : angle 1.25002 ( 4) hydrogen bonds : bond 0.03475 ( 119) hydrogen bonds : angle 6.51398 ( 312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: a 137 PHE cc_start: 0.2741 (t80) cc_final: 0.2306 (t80) REVERT: b 82 LEU cc_start: 0.8263 (mp) cc_final: 0.8054 (mp) outliers start: 20 outliers final: 9 residues processed: 96 average time/residue: 0.4224 time to fit residues: 42.1445 Evaluate side-chains 86 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain a residue 174 ILE Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 189 LEU Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 200 HIS Chi-restraints excluded: chain b residue 218 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 0.0570 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.167304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.135565 restraints weight = 5639.735| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.86 r_work: 0.3970 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3724 Z= 0.153 Angle : 0.643 7.346 5050 Z= 0.323 Chirality : 0.047 0.192 554 Planarity : 0.005 0.044 620 Dihedral : 4.395 16.924 481 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 92.00 % Rotamer: Outliers : 5.01 % Allowed : 26.32 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.39), residues: 425 helix: -3.60 (1.35), residues: 7 sheet: -0.35 (0.35), residues: 214 loop : -2.17 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 16 TYR 0.009 0.001 TYR b 49 PHE 0.013 0.002 PHE a 123 TRP 0.016 0.001 TRP a 109 HIS 0.002 0.001 HIS a 202 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3722) covalent geometry : angle 0.64269 ( 5046) SS BOND : bond 0.00341 ( 2) SS BOND : angle 1.16753 ( 4) hydrogen bonds : bond 0.03333 ( 119) hydrogen bonds : angle 6.20662 ( 312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.121 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 91 average time/residue: 0.5068 time to fit residues: 47.6610 Evaluate side-chains 79 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 146 CYS Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 189 LEU Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.167830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.136194 restraints weight = 5628.121| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.88 r_work: 0.3986 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3724 Z= 0.137 Angle : 0.619 7.978 5050 Z= 0.315 Chirality : 0.046 0.190 554 Planarity : 0.005 0.044 620 Dihedral : 4.233 16.466 481 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.59 % Favored : 93.18 % Rotamer: Outliers : 4.51 % Allowed : 28.07 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.39), residues: 425 helix: -3.35 (1.55), residues: 7 sheet: -0.23 (0.36), residues: 212 loop : -2.27 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 74 TYR 0.016 0.001 TYR a 153 PHE 0.007 0.001 PHE a 47 TRP 0.017 0.001 TRP a 109 HIS 0.002 0.001 HIS a 202 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3722) covalent geometry : angle 0.61876 ( 5046) SS BOND : bond 0.00259 ( 2) SS BOND : angle 1.05673 ( 4) hydrogen bonds : bond 0.03215 ( 119) hydrogen bonds : angle 6.06417 ( 312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.106 Fit side-chains REVERT: a 107 SER cc_start: 0.8053 (p) cc_final: 0.7835 (t) REVERT: b 184 MET cc_start: 0.8343 (ptp) cc_final: 0.8019 (ptm) outliers start: 18 outliers final: 7 residues processed: 86 average time/residue: 0.4522 time to fit residues: 40.2929 Evaluate side-chains 78 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain a residue 174 ILE Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 146 CYS Chi-restraints excluded: chain b residue 189 LEU Chi-restraints excluded: chain b residue 191 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 161 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 = 0.4386 r_free = 0.4386 target = 0.165306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.133106 restraints weight = 5669.958| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.88 r_work: 0.3901 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3724 Z= 0.202 Angle : 0.699 10.273 5050 Z= 0.349 Chirality : 0.047 0.194 554 Planarity : 0.005 0.043 620 Dihedral : 4.515 15.957 481 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.94 % Favored : 90.82 % Rotamer: Outliers : 4.76 % Allowed : 29.32 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.39), residues: 425 helix: -3.44 (1.37), residues: 7 sheet: -0.37 (0.36), residues: 213 loop : -2.26 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 16 TYR 0.025 0.002 TYR a 153 PHE 0.014 0.002 PHE a 123 TRP 0.017 0.002 TRP b 76 HIS 0.004 0.001 HIS b 159 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 3722) covalent geometry : angle 0.69799 ( 5046) SS BOND : bond 0.00356 ( 2) SS BOND : angle 1.31083 ( 4) hydrogen bonds : bond 0.03412 ( 119) hydrogen bonds : angle 6.34620 ( 312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.153 Fit side-chains REVERT: b 184 MET cc_start: 0.8349 (ptp) cc_final: 0.8066 (ptm) outliers start: 19 outliers final: 14 residues processed: 79 average time/residue: 0.4501 time to fit residues: 36.8536 Evaluate side-chains 80 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 174 ILE Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 13 ARG Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 146 CYS Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 189 LEU Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 202 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.0670 chunk 1 optimal weight: 20.0000 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 29 ASN b 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.167146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.134768 restraints weight = 5692.334| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.96 r_work: 0.3986 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3724 Z= 0.139 Angle : 0.661 9.110 5050 Z= 0.329 Chirality : 0.046 0.191 554 Planarity : 0.005 0.045 620 Dihedral : 4.347 16.017 481 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.06 % Favored : 92.71 % Rotamer: Outliers : 5.26 % Allowed : 27.57 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.39), residues: 425 helix: -2.93 (1.63), residues: 7 sheet: -0.20 (0.36), residues: 212 loop : -2.26 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 16 TYR 0.010 0.001 TYR a 153 PHE 0.009 0.001 PHE a 152 TRP 0.021 0.001 TRP b 76 HIS 0.004 0.001 HIS b 159 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3722) covalent geometry : angle 0.66017 ( 5046) SS BOND : bond 0.00260 ( 2) SS BOND : angle 1.07161 ( 4) hydrogen bonds : bond 0.03186 ( 119) hydrogen bonds : angle 6.11991 ( 312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.148 Fit side-chains REVERT: b 161 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7202 (mp-120) REVERT: b 184 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7952 (ptm) outliers start: 21 outliers final: 12 residues processed: 90 average time/residue: 0.4066 time to fit residues: 38.0024 Evaluate side-chains 83 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 174 ILE Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 61 SER Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 146 CYS Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 161 GLN Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 202 CYS Chi-restraints excluded: chain b residue 218 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4403 r_free = 0.4403 target = 0.166913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.134933 restraints weight = 5811.526| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.94 r_work: 0.3966 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3724 Z= 0.174 Angle : 0.700 10.203 5050 Z= 0.347 Chirality : 0.046 0.192 554 Planarity : 0.005 0.046 620 Dihedral : 4.448 16.101 481 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 92.00 % Rotamer: Outliers : 5.26 % Allowed : 29.07 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.39), residues: 425 helix: -3.10 (1.65), residues: 7 sheet: -0.21 (0.36), residues: 213 loop : -2.24 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 16 TYR 0.013 0.002 TYR a 32 PHE 0.015 0.002 PHE a 123 TRP 0.027 0.002 TRP b 76 HIS 0.003 0.001 HIS b 159 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3722) covalent geometry : angle 0.69946 ( 5046) SS BOND : bond 0.00300 ( 2) SS BOND : angle 1.19490 ( 4) hydrogen bonds : bond 0.03419 ( 119) hydrogen bonds : angle 6.21148 ( 312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.147 Fit side-chains REVERT: a 185 VAL cc_start: 0.8237 (t) cc_final: 0.7974 (m) REVERT: b 184 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7924 (ptm) outliers start: 21 outliers final: 13 residues processed: 83 average time/residue: 0.4365 time to fit residues: 37.7363 Evaluate side-chains 83 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 174 ILE Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 146 CYS Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 189 LEU Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 200 HIS Chi-restraints excluded: chain b residue 202 CYS Chi-restraints excluded: chain b residue 218 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 0.0470 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.167209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.135237 restraints weight = 5676.995| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.89 r_work: 0.3986 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3724 Z= 0.149 Angle : 0.702 10.181 5050 Z= 0.343 Chirality : 0.046 0.187 554 Planarity : 0.005 0.049 620 Dihedral : 4.336 15.447 481 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.06 % Favored : 92.71 % Rotamer: Outliers : 4.01 % Allowed : 30.83 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.39), residues: 425 helix: -3.03 (1.76), residues: 7 sheet: -0.13 (0.36), residues: 210 loop : -2.24 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 16 TYR 0.011 0.001 TYR a 32 PHE 0.015 0.002 PHE a 137 TRP 0.031 0.001 TRP b 76 HIS 0.002 0.001 HIS b 159 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3722) covalent geometry : angle 0.70168 ( 5046) SS BOND : bond 0.00255 ( 2) SS BOND : angle 1.06770 ( 4) hydrogen bonds : bond 0.03237 ( 119) hydrogen bonds : angle 6.08291 ( 312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.089 Fit side-chains REVERT: a 139 MET cc_start: 0.4874 (mmt) cc_final: 0.4521 (mmm) REVERT: b 40 GLU cc_start: 0.7483 (mp0) cc_final: 0.6986 (mp0) REVERT: b 184 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7947 (ptm) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.4174 time to fit residues: 36.4981 Evaluate side-chains 84 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 174 ILE Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 202 CYS Chi-restraints excluded: chain b residue 218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 4 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.167498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.135654 restraints weight = 5675.330| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.90 r_work: 0.3968 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3724 Z= 0.165 Angle : 0.733 10.233 5050 Z= 0.360 Chirality : 0.047 0.188 554 Planarity : 0.005 0.048 620 Dihedral : 4.420 15.504 481 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.53 % Favored : 92.24 % Rotamer: Outliers : 3.01 % Allowed : 31.58 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.40), residues: 425 helix: -2.90 (1.72), residues: 7 sheet: -0.15 (0.36), residues: 210 loop : -2.18 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 16 TYR 0.011 0.001 TYR a 32 PHE 0.016 0.002 PHE a 123 TRP 0.035 0.002 TRP b 76 HIS 0.003 0.001 HIS b 159 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 3722) covalent geometry : angle 0.73235 ( 5046) SS BOND : bond 0.00285 ( 2) SS BOND : angle 1.12745 ( 4) hydrogen bonds : bond 0.03276 ( 119) hydrogen bonds : angle 6.09504 ( 312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.175 Fit side-chains REVERT: a 139 MET cc_start: 0.5172 (OUTLIER) cc_final: 0.4834 (mmm) REVERT: b 40 GLU cc_start: 0.7491 (mp0) cc_final: 0.6975 (mp0) REVERT: b 184 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7946 (ptm) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.4329 time to fit residues: 34.6193 Evaluate side-chains 81 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain a residue 139 MET Chi-restraints excluded: chain a residue 174 ILE Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 202 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.0270 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.167915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.137003 restraints weight = 5715.195| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.00 r_work: 0.3953 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3724 Z= 0.135 Angle : 0.742 12.211 5050 Z= 0.362 Chirality : 0.047 0.192 554 Planarity : 0.005 0.050 620 Dihedral : 4.259 15.112 481 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.01 % Allowed : 32.08 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.40), residues: 425 helix: -2.70 (1.82), residues: 7 sheet: 0.05 (0.37), residues: 208 loop : -2.19 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 16 TYR 0.010 0.001 TYR a 32 PHE 0.015 0.001 PHE a 137 TRP 0.045 0.002 TRP b 76 HIS 0.003 0.001 HIS b 159 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3722) covalent geometry : angle 0.74167 ( 5046) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.91066 ( 4) hydrogen bonds : bond 0.03137 ( 119) hydrogen bonds : angle 5.89187 ( 312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.118 Fit side-chains REVERT: a 139 MET cc_start: 0.5230 (mmt) cc_final: 0.4927 (mmm) REVERT: b 184 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7973 (ptm) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.3692 time to fit residues: 30.8882 Evaluate side-chains 79 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 174 ILE Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 147 LEU Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 202 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.167757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.136742 restraints weight = 5582.312| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.96 r_work: 0.3950 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3724 Z= 0.144 Angle : 0.739 12.170 5050 Z= 0.363 Chirality : 0.047 0.189 554 Planarity : 0.005 0.049 620 Dihedral : 4.263 15.014 481 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.51 % Allowed : 33.33 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.40), residues: 425 helix: -2.48 (1.79), residues: 7 sheet: 0.04 (0.37), residues: 209 loop : -2.15 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 16 TYR 0.012 0.001 TYR b 69 PHE 0.019 0.002 PHE a 123 TRP 0.042 0.002 TRP b 76 HIS 0.003 0.001 HIS b 159 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3722) covalent geometry : angle 0.73831 ( 5046) SS BOND : bond 0.00245 ( 2) SS BOND : angle 0.96958 ( 4) hydrogen bonds : bond 0.03279 ( 119) hydrogen bonds : angle 5.89213 ( 312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.81 seconds wall clock time: 32 minutes 17.32 seconds (1937.32 seconds total)