Starting phenix.real_space_refine on Mon Feb 10 23:27:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnn_34917/02_2025/8hnn_34917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnn_34917/02_2025/8hnn_34917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnn_34917/02_2025/8hnn_34917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnn_34917/02_2025/8hnn_34917.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnn_34917/02_2025/8hnn_34917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnn_34917/02_2025/8hnn_34917.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.080 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 17 5.16 5 Cl 2 4.86 5 C 1993 2.51 5 N 527 2.21 5 O 524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3063 Number of models: 1 Model: "" Number of chains: 3 Chain: "N" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 852 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2150 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'43I': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.91, per 1000 atoms: 0.95 Number of scatterers: 3063 At special positions: 0 Unit cell: (71.4, 52.7, 123.25, 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) Cl 2 17.00 S 17 16.00 O 524 8.00 N 527 7.00 C 1993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " 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: 0.84 Conformation dependent library (CDL) restraints added in 348.2 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 4 sheets defined 56.6% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 55 through 80 Processing helix chain 'R' and resid 86 through 105 removed outlier: 3.851A pdb=" N ASP R 99 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU R 101 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 115 removed outlier: 3.909A pdb=" N TRP R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 154 removed outlier: 4.064A pdb=" N PHE R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR R 136 " --> pdb=" O ASN R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 189 Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 211 through 244 Proline residue: R 227 - end of helix removed outlier: 3.889A pdb=" N SER R 244 " --> pdb=" O ALA R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 291 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 300 through 329 removed outlier: 4.207A pdb=" N CYS R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix removed outlier: 3.675A pdb=" N VAL R 329 " --> pdb=" O LEU R 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 4 through 9 Processing sheet with id=AA2, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.842A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET N 36 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU N 33 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG N 102 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP N 35 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.842A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET N 36 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU N 33 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG N 102 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP N 35 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 190 through 191 removed outlier: 4.145A pdb=" N SER R 191 " --> pdb=" O GLN R 204 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN R 204 " --> pdb=" O SER R 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 205 hydrogen bonds defined for protein. 591 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: 0.76 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 972 1.34 - 1.46: 711 1.46 - 1.58: 1424 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3131 Sorted by residual: bond pdb=" C19 43I R 401 " pdb=" C22 43I R 401 " ideal model delta sigma weight residual 1.437 1.379 0.058 2.00e-02 2.50e+03 8.44e+00 bond pdb=" C10 43I R 401 " pdb=" C11 43I R 401 " ideal model delta sigma weight residual 1.524 1.488 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C22 43I R 401 " pdb="CL2 43I R 401 " ideal model delta sigma weight residual 1.763 1.730 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C23 43I R 401 " pdb=" N6 43I R 401 " ideal model delta sigma weight residual 1.347 1.318 0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C14 43I R 401 " pdb=" C15 43I R 401 " ideal model delta sigma weight residual 1.388 1.359 0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 3126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4138 1.61 - 3.21: 101 3.21 - 4.82: 17 4.82 - 6.42: 14 6.42 - 8.03: 2 Bond angle restraints: 4272 Sorted by residual: angle pdb=" C8 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " ideal model delta sigma weight residual 115.50 123.35 -7.85 3.00e+00 1.11e-01 6.84e+00 angle pdb=" C LEU R 225 " pdb=" N LEU R 226 " pdb=" CA LEU R 226 " ideal model delta sigma weight residual 121.80 115.59 6.21 2.44e+00 1.68e-01 6.47e+00 angle pdb=" C HIS R 94 " pdb=" N LEU R 95 " pdb=" CA LEU R 95 " ideal model delta sigma weight residual 121.58 117.00 4.58 1.95e+00 2.63e-01 5.52e+00 angle pdb=" CA LEU R 95 " pdb=" CB LEU R 95 " pdb=" CG LEU R 95 " ideal model delta sigma weight residual 116.30 124.33 -8.03 3.50e+00 8.16e-02 5.26e+00 angle pdb=" C19 43I R 401 " pdb=" N1 43I R 401 " pdb=" C5 43I R 401 " ideal model delta sigma weight residual 118.45 124.82 -6.37 3.00e+00 1.11e-01 4.50e+00 ... (remaining 4267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.68: 1847 32.68 - 65.37: 34 65.37 - 98.05: 4 98.05 - 130.74: 6 130.74 - 163.42: 2 Dihedral angle restraints: 1893 sinusoidal: 765 harmonic: 1128 Sorted by residual: dihedral pdb=" CB CYS R 124 " pdb=" SG CYS R 124 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual 93.00 -178.02 -88.98 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" C11 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " pdb=" C3 43I R 401 " ideal model delta sinusoidal sigma weight residual 198.38 34.96 163.42 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C11 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " pdb=" C6 43I R 401 " ideal model delta sinusoidal sigma weight residual 63.87 -94.22 158.09 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 1890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.818: 507 0.818 - 1.635: 0 1.635 - 2.453: 0 2.453 - 3.271: 0 3.271 - 4.089: 1 Chirality restraints: 508 Sorted by residual: chirality pdb=" C7 43I R 401 " pdb=" C11 43I R 401 " pdb=" C8 43I R 401 " pdb=" N2 43I R 401 " both_signs ideal model delta sigma weight residual False 2.33 -1.76 4.09 2.00e-01 2.50e+01 4.18e+02 chirality pdb=" CG LEU R 321 " pdb=" CB LEU R 321 " pdb=" CD1 LEU R 321 " pdb=" CD2 LEU R 321 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LEU R 106 " pdb=" N LEU R 106 " pdb=" C LEU R 106 " pdb=" CB LEU R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 505 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 222 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ALA R 222 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA R 222 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY R 223 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 196 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C GLU R 196 " 0.022 2.00e-02 2.50e+03 pdb=" O GLU R 196 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG R 197 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 135 " 0.010 2.00e-02 2.50e+03 7.74e-03 1.05e+00 pdb=" CG PHE R 135 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE R 135 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 135 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 135 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 135 " 0.004 2.00e-02 2.50e+03 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 318 2.74 - 3.28: 2951 3.28 - 3.82: 4849 3.82 - 4.36: 5235 4.36 - 4.90: 9449 Nonbonded interactions: 22802 Sorted by model distance: nonbonded pdb=" O ALA R 273 " pdb=" OG1 THR R 277 " model vdw 2.206 3.040 nonbonded pdb=" NZ LYS R 125 " pdb=" O LEU R 190 " model vdw 2.272 3.120 nonbonded pdb=" OG SER N 9 " pdb=" OG SER N 23 " model vdw 2.287 3.040 nonbonded pdb=" O GLN R 158 " pdb=" NH1 ARG R 162 " model vdw 2.317 3.120 nonbonded pdb=" O GLU R 253 " pdb=" ND2 ASN R 257 " model vdw 2.351 3.120 ... (remaining 22797 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 12.530 Find NCS groups from input model: 0.020 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3131 Z= 0.251 Angle : 0.688 8.025 4272 Z= 0.338 Chirality : 0.186 4.089 508 Planarity : 0.003 0.021 521 Dihedral : 17.325 163.420 1165 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.44), residues: 386 helix: 1.05 (0.35), residues: 217 sheet: 2.72 (0.80), residues: 44 loop : -1.64 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.010 0.001 TYR R 233 ARG 0.002 0.000 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 101 TYR cc_start: 0.8965 (p90) cc_final: 0.8449 (p90) REVERT: N 113 TRP cc_start: 0.8339 (m100) cc_final: 0.7985 (m-90) REVERT: R 254 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7233 (ttpt) REVERT: R 274 LEU cc_start: 0.8379 (tt) cc_final: 0.8176 (tp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1210 time to fit residues: 9.2394 Evaluate side-chains 56 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.0270 chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN R 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.196299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128902 restraints weight = 2875.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133738 restraints weight = 1764.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136632 restraints weight = 1369.246| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3131 Z= 0.185 Angle : 0.627 8.419 4272 Z= 0.298 Chirality : 0.039 0.119 508 Planarity : 0.003 0.021 521 Dihedral : 13.061 139.782 538 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.88 % Allowed : 8.97 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.44), residues: 386 helix: 1.29 (0.36), residues: 217 sheet: 2.21 (0.77), residues: 49 loop : -1.28 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.020 0.002 PHE R 328 TYR 0.009 0.001 TYR R 233 ARG 0.002 0.000 ARG R 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 MET cc_start: 0.7842 (mtt) cc_final: 0.7549 (mmm) REVERT: N 113 TRP cc_start: 0.8306 (m100) cc_final: 0.7922 (m-90) REVERT: R 189 PHE cc_start: 0.8022 (m-10) cc_final: 0.7772 (m-10) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.1178 time to fit residues: 8.9680 Evaluate side-chains 60 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 243 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.190248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122877 restraints weight = 2879.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127291 restraints weight = 1858.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129767 restraints weight = 1472.259| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3131 Z= 0.230 Angle : 0.643 9.251 4272 Z= 0.311 Chirality : 0.040 0.126 508 Planarity : 0.003 0.020 521 Dihedral : 12.630 139.686 538 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.53 % Allowed : 14.74 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.44), residues: 386 helix: 1.27 (0.37), residues: 218 sheet: 2.13 (0.77), residues: 49 loop : -1.24 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 318 PHE 0.021 0.002 PHE R 187 TYR 0.011 0.001 TYR N 101 ARG 0.002 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8309 (m100) cc_final: 0.7901 (m-90) REVERT: R 92 LEU cc_start: 0.8465 (mm) cc_final: 0.8242 (mt) REVERT: R 189 PHE cc_start: 0.8102 (m-10) cc_final: 0.7793 (m-10) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.1143 time to fit residues: 8.9572 Evaluate side-chains 62 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.190896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123004 restraints weight = 2915.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127512 restraints weight = 1829.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129833 restraints weight = 1437.423| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3131 Z= 0.219 Angle : 0.630 9.357 4272 Z= 0.304 Chirality : 0.039 0.125 508 Planarity : 0.003 0.021 521 Dihedral : 12.444 140.941 538 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.17 % Allowed : 17.95 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.44), residues: 386 helix: 1.33 (0.37), residues: 218 sheet: 2.23 (0.76), residues: 49 loop : -1.23 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.016 0.001 PHE R 135 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8307 (m100) cc_final: 0.7897 (m-90) REVERT: R 189 PHE cc_start: 0.8059 (m-10) cc_final: 0.7709 (m-10) outliers start: 13 outliers final: 10 residues processed: 62 average time/residue: 0.1119 time to fit residues: 9.0945 Evaluate side-chains 67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 75 ASN R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.195961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133591 restraints weight = 2876.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137839 restraints weight = 1822.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140493 restraints weight = 1445.617| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3131 Z= 0.257 Angle : 0.675 9.766 4272 Z= 0.322 Chirality : 0.040 0.132 508 Planarity : 0.003 0.020 521 Dihedral : 12.255 142.289 538 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.17 % Allowed : 18.91 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.44), residues: 386 helix: 1.24 (0.36), residues: 218 sheet: 2.22 (0.75), residues: 49 loop : -1.31 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.018 0.002 PHE R 135 TYR 0.012 0.001 TYR N 101 ARG 0.002 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8251 (m100) cc_final: 0.7939 (m-90) REVERT: R 189 PHE cc_start: 0.8163 (m-10) cc_final: 0.7876 (m-10) outliers start: 13 outliers final: 12 residues processed: 62 average time/residue: 0.1102 time to fit residues: 8.9874 Evaluate side-chains 66 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.188884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121970 restraints weight = 2998.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125774 restraints weight = 1998.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128185 restraints weight = 1611.936| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3131 Z= 0.197 Angle : 0.627 9.388 4272 Z= 0.298 Chirality : 0.038 0.121 508 Planarity : 0.003 0.021 521 Dihedral : 12.083 146.606 538 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.45 % Allowed : 18.27 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.44), residues: 386 helix: 1.36 (0.37), residues: 218 sheet: 2.25 (0.75), residues: 49 loop : -1.27 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.016 0.001 PHE R 135 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8267 (m100) cc_final: 0.7943 (m-90) REVERT: R 187 PHE cc_start: 0.8289 (m-80) cc_final: 0.7923 (m-80) REVERT: R 189 PHE cc_start: 0.8106 (m-10) cc_final: 0.7796 (m-10) outliers start: 17 outliers final: 10 residues processed: 62 average time/residue: 0.1422 time to fit residues: 11.7434 Evaluate side-chains 64 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.200419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139688 restraints weight = 2873.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144160 restraints weight = 1775.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146479 restraints weight = 1390.060| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3131 Z= 0.204 Angle : 0.624 9.492 4272 Z= 0.299 Chirality : 0.038 0.121 508 Planarity : 0.003 0.021 521 Dihedral : 12.199 151.136 538 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.49 % Allowed : 19.55 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.44), residues: 386 helix: 1.39 (0.37), residues: 218 sheet: 2.30 (0.75), residues: 49 loop : -1.34 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8258 (m100) cc_final: 0.7953 (m-90) REVERT: R 187 PHE cc_start: 0.8416 (m-80) cc_final: 0.8075 (m-80) REVERT: R 189 PHE cc_start: 0.8121 (m-10) cc_final: 0.7821 (m-10) outliers start: 14 outliers final: 11 residues processed: 61 average time/residue: 0.1146 time to fit residues: 9.0873 Evaluate side-chains 65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.200416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138782 restraints weight = 2861.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143266 restraints weight = 1790.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145497 restraints weight = 1411.537| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3131 Z= 0.174 Angle : 0.635 12.481 4272 Z= 0.295 Chirality : 0.038 0.115 508 Planarity : 0.003 0.021 521 Dihedral : 12.259 154.284 538 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.13 % Allowed : 19.55 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.44), residues: 386 helix: 1.48 (0.37), residues: 218 sheet: 2.34 (0.76), residues: 49 loop : -1.34 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.015 0.001 PHE R 135 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8230 (m100) cc_final: 0.7943 (m-90) REVERT: R 187 PHE cc_start: 0.8404 (m-80) cc_final: 0.8089 (m-80) REVERT: R 189 PHE cc_start: 0.8088 (m-10) cc_final: 0.7789 (m-10) outliers start: 16 outliers final: 15 residues processed: 62 average time/residue: 0.1079 time to fit residues: 8.7376 Evaluate side-chains 70 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.198261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135966 restraints weight = 2885.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.140522 restraints weight = 1806.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143172 restraints weight = 1420.327| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3131 Z= 0.202 Angle : 0.654 12.175 4272 Z= 0.305 Chirality : 0.038 0.121 508 Planarity : 0.003 0.021 521 Dihedral : 12.496 158.818 538 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.81 % Allowed : 21.47 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.44), residues: 386 helix: 1.40 (0.37), residues: 218 sheet: 2.34 (0.75), residues: 49 loop : -1.41 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8275 (m100) cc_final: 0.7967 (m-90) REVERT: R 189 PHE cc_start: 0.8097 (m-10) cc_final: 0.7775 (m-10) outliers start: 15 outliers final: 14 residues processed: 60 average time/residue: 0.1146 time to fit residues: 8.9978 Evaluate side-chains 68 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.194725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132818 restraints weight = 2841.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136963 restraints weight = 1818.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139031 restraints weight = 1454.000| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3131 Z= 0.257 Angle : 0.690 12.364 4272 Z= 0.326 Chirality : 0.040 0.133 508 Planarity : 0.003 0.020 521 Dihedral : 12.874 164.529 538 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.17 % Allowed : 21.79 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.44), residues: 386 helix: 1.31 (0.36), residues: 218 sheet: 2.33 (0.75), residues: 49 loop : -1.46 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.025 0.002 PHE R 187 TYR 0.011 0.001 TYR R 150 ARG 0.002 0.000 ARG R 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8251 (m100) cc_final: 0.7949 (m-90) REVERT: R 189 PHE cc_start: 0.8169 (m-10) cc_final: 0.7862 (m-10) outliers start: 13 outliers final: 12 residues processed: 62 average time/residue: 0.1187 time to fit residues: 9.7898 Evaluate side-chains 67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.187635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124539 restraints weight = 2920.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129266 restraints weight = 2858.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129721 restraints weight = 1833.737| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3131 Z= 0.233 Angle : 0.679 12.104 4272 Z= 0.321 Chirality : 0.039 0.122 508 Planarity : 0.003 0.020 521 Dihedral : 13.040 168.547 538 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.17 % Allowed : 22.12 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.44), residues: 386 helix: 1.34 (0.37), residues: 218 sheet: 2.31 (0.75), residues: 49 loop : -1.50 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.024 0.002 TYR R 326 ARG 0.002 0.000 ARG R 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1348.33 seconds wall clock time: 24 minutes 51.11 seconds (1491.11 seconds total)