Starting phenix.real_space_refine on Tue Feb 11 21:07:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iow_35627/02_2025/8iow_35627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iow_35627/02_2025/8iow_35627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iow_35627/02_2025/8iow_35627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iow_35627/02_2025/8iow_35627.map" model { file = "/net/cci-nas-00/data/ceres_data/8iow_35627/02_2025/8iow_35627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iow_35627/02_2025/8iow_35627.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3017 atoms to isotropic. 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 18 5.16 5 C 2628 2.51 5 N 721 2.21 5 O 811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 4178 Number of models: 1 Model: "" Number of chains: 5 Chain: "I" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 863 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "D2" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 107 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "H" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1561 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.70, per 1000 atoms: 0.89 Number of scatterers: 4178 At special positions: 0 Unit cell: (58.22, 67.24, 104.96, 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 18 16.00 O 811 8.00 N 721 7.00 C 2628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYSD2 121 " - pdb=" SG CYSD2 132 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 199 " 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 Links applied NAG-ASN " NAG I 401 " - " ASN I 221 " " NAG I 402 " - " ASN I 245 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 423.1 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 15 sheets defined 6.7% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.300A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.945A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 4.049A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 192 Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing sheet with id=AA1, first strand: chain 'I' and resid 223 through 225 Processing sheet with id=AA2, first strand: chain 'I' and resid 266 through 269 removed outlier: 3.856A pdb=" N THR I 266 " --> pdb=" O TYR I 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.959A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.423A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.604A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.426A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.720A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY H 50 " --> pdb=" O GLY H 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 73 Processing sheet with id=AB4, first strand: chain 'H' and resid 123 through 127 removed outlier: 5.034A pdb=" N ALA H 140 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL H 187 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY H 142 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL H 185 " --> pdb=" O GLY H 142 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU H 144 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER H 183 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS H 146 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU H 181 " --> pdb=" O LYS H 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 123 through 127 removed outlier: 5.034A pdb=" N ALA H 140 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL H 187 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY H 142 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL H 185 " --> pdb=" O GLY H 142 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU H 144 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER H 183 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS H 146 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU H 181 " --> pdb=" O LYS H 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 153 through 157 removed outlier: 3.547A pdb=" N THR H 154 " --> pdb=" O ASN H 202 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR H 197 " --> pdb=" O VAL H 214 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 300 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: 1.17 Time building geometry restraints manager: 1.10 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: 1330 1.34 - 1.46: 973 1.46 - 1.58: 1954 1.58 - 1.69: 1 1.69 - 1.81: 24 Bond restraints: 4282 Sorted by residual: bond pdb=" C1 NAG I 402 " pdb=" O5 NAG I 402 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" CA VAL I 227 " pdb=" CB VAL I 227 " ideal model delta sigma weight residual 1.530 1.555 -0.025 1.11e-02 8.12e+03 4.99e+00 bond pdb=" CB PRO I 308 " pdb=" CG PRO I 308 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.69e+00 bond pdb=" C1 NAG I 401 " pdb=" O5 NAG I 401 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" SD MET I 269 " pdb=" CE MET I 269 " ideal model delta sigma weight residual 1.791 1.750 0.041 2.50e-02 1.60e+03 2.64e+00 ... (remaining 4277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 5557 2.04 - 4.07: 208 4.07 - 6.11: 33 6.11 - 8.15: 17 8.15 - 10.19: 3 Bond angle restraints: 5818 Sorted by residual: angle pdb=" CA PRO I 308 " pdb=" N PRO I 308 " pdb=" CD PRO I 308 " ideal model delta sigma weight residual 112.00 105.65 6.35 1.40e+00 5.10e-01 2.06e+01 angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 112.96 109.10 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" C GLY L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 128.20 -6.66 1.91e+00 2.74e-01 1.22e+01 angle pdb=" CG ARG H 26 " pdb=" CD ARG H 26 " pdb=" NE ARG H 26 " ideal model delta sigma weight residual 112.00 119.57 -7.57 2.20e+00 2.07e-01 1.18e+01 angle pdb=" CA TYR I 257 " pdb=" CB TYR I 257 " pdb=" CG TYR I 257 " ideal model delta sigma weight residual 113.90 120.07 -6.17 1.80e+00 3.09e-01 1.17e+01 ... (remaining 5813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 2253 16.03 - 32.05: 238 32.05 - 48.08: 59 48.08 - 64.10: 16 64.10 - 80.13: 5 Dihedral angle restraints: 2571 sinusoidal: 1027 harmonic: 1544 Sorted by residual: dihedral pdb=" CA VAL H 114 " pdb=" C VAL H 114 " pdb=" N SER H 115 " pdb=" CA SER H 115 " ideal model delta harmonic sigma weight residual -180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CB CYS H 143 " pdb=" SG CYS H 143 " pdb=" SG CYS H 199 " pdb=" CB CYS H 199 " ideal model delta sinusoidal sigma weight residual -86.00 -39.25 -46.75 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" CB CYSD2 121 " pdb=" SG CYSD2 121 " pdb=" SG CYSD2 132 " pdb=" CB CYSD2 132 " ideal model delta sinusoidal sigma weight residual -86.00 -131.40 45.40 1 1.00e+01 1.00e-02 2.86e+01 ... (remaining 2568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 536 0.075 - 0.151: 95 0.151 - 0.226: 4 0.226 - 0.301: 4 0.301 - 0.376: 2 Chirality restraints: 641 Sorted by residual: chirality pdb=" C1 NAG I 402 " pdb=" ND2 ASN I 245 " pdb=" C2 NAG I 402 " pdb=" O5 NAG I 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB THR I 266 " pdb=" CA THR I 266 " pdb=" OG1 THR I 266 " pdb=" CG2 THR I 266 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE I 213 " pdb=" CA ILE I 213 " pdb=" CG1 ILE I 213 " pdb=" CG2 ILE I 213 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 638 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 307 " 0.090 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO I 308 " -0.229 5.00e-02 4.00e+02 pdb=" CA PRO I 308 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO I 308 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 53 " -0.034 2.00e-02 2.50e+03 2.88e-02 2.08e+01 pdb=" CG TRP H 53 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP H 53 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP H 53 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 53 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 53 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 53 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 53 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 53 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP H 53 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO L 95 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.042 5.00e-02 4.00e+02 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1061 2.80 - 3.32: 3522 3.32 - 3.85: 7158 3.85 - 4.37: 8163 4.37 - 4.90: 14551 Nonbonded interactions: 34455 Sorted by model distance: nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP L 170 " pdb=" OG1 THR L 172 " model vdw 2.291 3.040 nonbonded pdb=" NH1 ARG L 61 " pdb=" OD2 ASP L 82 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASN H 202 " pdb=" NZ LYS H 204 " model vdw 2.330 3.120 nonbonded pdb=" O SERD2 128 " pdb=" OG SERD2 128 " model vdw 2.335 3.040 ... (remaining 34450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.680 Find NCS groups from input model: 0.070 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.007 0.096 4282 Z= 0.421 Angle : 0.984 10.186 5818 Z= 0.530 Chirality : 0.061 0.376 641 Planarity : 0.009 0.132 745 Dihedral : 14.462 80.127 1562 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.31 (0.35), residues: 527 helix: -2.63 (1.00), residues: 14 sheet: -1.33 (0.34), residues: 218 loop : -1.61 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP H 53 HIS 0.005 0.001 HIS I 288 PHE 0.036 0.004 PHE L 94 TYR 0.033 0.003 TYR L 173 ARG 0.016 0.002 ARG I 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.435 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2428 time to fit residues: 21.2012 Evaluate side-chains 65 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 242 HIS L 90 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.171789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.144945 restraints weight = 4702.075| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.92 r_work: 0.3520 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4282 Z= 0.263 Angle : 0.656 8.033 5818 Z= 0.345 Chirality : 0.047 0.285 641 Planarity : 0.006 0.070 745 Dihedral : 6.791 46.008 617 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.52 % Allowed : 8.46 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.76 (0.37), residues: 527 helix: -1.86 (1.15), residues: 14 sheet: -1.11 (0.34), residues: 224 loop : -1.09 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 53 HIS 0.007 0.001 HIS L 189 PHE 0.029 0.002 PHE H 149 TYR 0.011 0.002 TYR L 173 ARG 0.006 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: I 287 ARG cc_start: 0.5939 (tpm170) cc_final: 0.5692 (tpm170) REVERT: L 79 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8196 (mm110) REVERT: L 182 SER cc_start: 0.8817 (t) cc_final: 0.8572 (p) REVERT: L 197 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8048 (p) REVERT: L 208 SER cc_start: 0.8239 (m) cc_final: 0.7996 (p) REVERT: H 180 SER cc_start: 0.8262 (t) cc_final: 0.7979 (p) outliers start: 7 outliers final: 4 residues processed: 85 average time/residue: 0.2383 time to fit residues: 24.0258 Evaluate side-chains 79 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain H residue 30 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.172998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144828 restraints weight = 4680.258| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.02 r_work: 0.3522 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4282 Z= 0.229 Angle : 0.609 7.152 5818 Z= 0.318 Chirality : 0.045 0.270 641 Planarity : 0.005 0.065 745 Dihedral : 5.874 34.545 617 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.52 % Allowed : 11.50 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.65 (0.37), residues: 527 helix: -1.61 (1.15), residues: 14 sheet: -1.10 (0.32), residues: 242 loop : -0.93 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.006 0.001 HIS L 189 PHE 0.025 0.002 PHE H 149 TYR 0.013 0.001 TYR L 173 ARG 0.007 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: I 276 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6827 (p90) REVERT: L 182 SER cc_start: 0.8847 (t) cc_final: 0.8604 (p) REVERT: L 190 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7973 (tptp) REVERT: L 197 THR cc_start: 0.8288 (m) cc_final: 0.7994 (p) REVERT: L 208 SER cc_start: 0.8161 (m) cc_final: 0.7897 (p) outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 0.2459 time to fit residues: 23.5424 Evaluate side-chains 76 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain H residue 30 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.0070 chunk 48 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141771 restraints weight = 4678.204| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.99 r_work: 0.3505 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4282 Z= 0.257 Angle : 0.608 7.326 5818 Z= 0.316 Chirality : 0.045 0.269 641 Planarity : 0.005 0.064 745 Dihedral : 5.832 33.512 617 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.60 % Allowed : 13.88 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.53 (0.37), residues: 527 helix: -1.51 (1.18), residues: 14 sheet: -0.91 (0.33), residues: 228 loop : -1.00 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.005 0.001 HIS L 189 PHE 0.026 0.002 PHE H 149 TYR 0.014 0.002 TYR L 173 ARG 0.004 0.001 ARG I 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: I 276 HIS cc_start: 0.7174 (OUTLIER) cc_final: 0.6860 (p90) REVERT: L 182 SER cc_start: 0.8878 (t) cc_final: 0.8675 (p) REVERT: L 190 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7905 (tptp) REVERT: L 197 THR cc_start: 0.8272 (m) cc_final: 0.8020 (p) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 0.2281 time to fit residues: 23.9449 Evaluate side-chains 84 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.0020 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.160880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131955 restraints weight = 4900.464| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.01 r_work: 0.3482 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4282 Z= 0.258 Angle : 0.610 7.195 5818 Z= 0.314 Chirality : 0.045 0.259 641 Planarity : 0.005 0.062 745 Dihedral : 5.790 34.175 617 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.17 % Allowed : 16.49 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.46 (0.37), residues: 527 helix: -1.31 (1.26), residues: 14 sheet: -0.84 (0.34), residues: 228 loop : -0.98 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 106 HIS 0.004 0.001 HIS L 189 PHE 0.025 0.002 PHE H 149 TYR 0.014 0.001 TYR L 173 ARG 0.007 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7296 (mm) REVERT: I 276 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6887 (p90) REVERT: L 182 SER cc_start: 0.8882 (t) cc_final: 0.8678 (p) REVERT: L 197 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8033 (p) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.2447 time to fit residues: 24.1953 Evaluate side-chains 85 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 156 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134941 restraints weight = 4822.765| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.98 r_work: 0.3511 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4282 Z= 0.223 Angle : 0.595 6.896 5818 Z= 0.307 Chirality : 0.045 0.249 641 Planarity : 0.005 0.062 745 Dihedral : 5.689 33.165 617 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.47 % Allowed : 16.27 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.34 (0.37), residues: 527 helix: -0.93 (1.36), residues: 14 sheet: -0.70 (0.34), residues: 227 loop : -0.97 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 106 HIS 0.004 0.001 HIS L 189 PHE 0.024 0.002 PHE H 149 TYR 0.012 0.001 TYR L 173 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7275 (mm) REVERT: I 276 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6837 (p90) REVERT: L 197 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8050 (p) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.2357 time to fit residues: 25.1156 Evaluate side-chains 86 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 15 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 275 HIS L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.171153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142836 restraints weight = 4694.689| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.05 r_work: 0.3554 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4282 Z= 0.194 Angle : 0.573 6.738 5818 Z= 0.295 Chirality : 0.044 0.237 641 Planarity : 0.005 0.061 745 Dihedral : 5.500 30.453 617 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.47 % Allowed : 17.57 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.22 (0.37), residues: 527 helix: -0.89 (1.36), residues: 14 sheet: -0.57 (0.34), residues: 230 loop : -0.94 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 233 HIS 0.003 0.001 HIS L 189 PHE 0.022 0.002 PHE H 149 TYR 0.012 0.001 TYR L 173 ARG 0.006 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7355 (mm) REVERT: I 276 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6898 (p90) REVERT: L 197 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7961 (p) REVERT: H 53 TRP cc_start: 0.8910 (OUTLIER) cc_final: 0.8499 (p90) REVERT: H 83 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6754 (mtt) outliers start: 16 outliers final: 8 residues processed: 85 average time/residue: 0.2493 time to fit residues: 25.0836 Evaluate side-chains 85 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137661 restraints weight = 4710.355| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.04 r_work: 0.3467 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4282 Z= 0.340 Angle : 0.657 7.943 5818 Z= 0.339 Chirality : 0.047 0.253 641 Planarity : 0.005 0.064 745 Dihedral : 5.916 36.678 617 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.04 % Allowed : 18.22 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.42 (0.37), residues: 527 helix: -1.19 (1.28), residues: 14 sheet: -0.70 (0.34), residues: 230 loop : -1.07 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 106 HIS 0.003 0.001 HIS L 189 PHE 0.028 0.002 PHE H 149 TYR 0.017 0.002 TYR L 173 ARG 0.005 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7296 (mm) REVERT: I 276 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6966 (p90) REVERT: L 197 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8048 (p) REVERT: H 53 TRP cc_start: 0.8990 (OUTLIER) cc_final: 0.8620 (p90) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.2576 time to fit residues: 25.8008 Evaluate side-chains 87 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 239 GLN L 90 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139851 restraints weight = 4694.779| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.00 r_work: 0.3482 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4282 Z= 0.263 Angle : 0.623 7.362 5818 Z= 0.320 Chirality : 0.045 0.234 641 Planarity : 0.005 0.060 745 Dihedral : 5.819 36.291 617 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.82 % Allowed : 19.31 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.37 (0.37), residues: 527 helix: -1.12 (1.29), residues: 14 sheet: -0.66 (0.34), residues: 227 loop : -1.04 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 233 HIS 0.003 0.001 HIS H 203 PHE 0.025 0.002 PHE H 149 TYR 0.014 0.002 TYR L 173 ARG 0.006 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7271 (mm) REVERT: I 276 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6895 (p90) REVERT: L 197 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8069 (p) REVERT: H 53 TRP cc_start: 0.8987 (OUTLIER) cc_final: 0.8556 (p90) REVERT: H 83 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7010 (mtt) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 0.2418 time to fit residues: 23.5112 Evaluate side-chains 86 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 51 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.167096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141639 restraints weight = 4791.243| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.90 r_work: 0.3478 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4282 Z= 0.259 Angle : 0.623 7.388 5818 Z= 0.319 Chirality : 0.045 0.228 641 Planarity : 0.005 0.062 745 Dihedral : 5.796 35.849 617 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.04 % Allowed : 18.87 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.39 (0.37), residues: 527 helix: -1.13 (1.29), residues: 14 sheet: -0.74 (0.34), residues: 233 loop : -0.98 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 233 HIS 0.002 0.001 HIS H 203 PHE 0.025 0.002 PHE H 149 TYR 0.014 0.002 TYR L 173 ARG 0.009 0.001 ARG H 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7246 (mm) REVERT: I 276 HIS cc_start: 0.7173 (OUTLIER) cc_final: 0.6889 (p90) REVERT: L 197 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8077 (p) REVERT: H 53 TRP cc_start: 0.8966 (OUTLIER) cc_final: 0.8554 (p90) REVERT: H 83 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7041 (mtt) outliers start: 14 outliers final: 8 residues processed: 85 average time/residue: 0.2451 time to fit residues: 24.6852 Evaluate side-chains 89 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 51 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 0.0070 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139502 restraints weight = 4814.681| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.03 r_work: 0.3517 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4282 Z= 0.163 Angle : 0.576 7.180 5818 Z= 0.294 Chirality : 0.043 0.203 641 Planarity : 0.005 0.060 745 Dihedral : 5.436 29.905 617 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.95 % Allowed : 19.96 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.19 (0.38), residues: 527 helix: -0.90 (1.34), residues: 14 sheet: -0.58 (0.34), residues: 233 loop : -0.88 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 233 HIS 0.002 0.000 HIS H 203 PHE 0.019 0.001 PHE H 149 TYR 0.011 0.001 TYR L 49 ARG 0.010 0.001 ARG H 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.34 seconds wall clock time: 53 minutes 40.11 seconds (3220.11 seconds total)