Starting phenix.real_space_refine on Fri Dec 27 11:23:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de9_27388/12_2024/8de9_27388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de9_27388/12_2024/8de9_27388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8de9_27388/12_2024/8de9_27388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de9_27388/12_2024/8de9_27388.map" model { file = "/net/cci-nas-00/data/ceres_data/8de9_27388/12_2024/8de9_27388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de9_27388/12_2024/8de9_27388.cif" } resolution = 3.4 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= 0.002 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 1 5.49 5 S 16 5.16 5 C 2760 2.51 5 N 626 2.21 5 O 709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4115 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2035 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2028 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' K': 3, 'PEV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.35, per 1000 atoms: 0.81 Number of scatterers: 4115 At special positions: 0 Unit cell: (80.514, 97.128, 79.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 16 16.00 P 1 15.00 O 709 8.00 N 626 7.00 C 2760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS B 93 " 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: 1.19 Conformation dependent library (CDL) restraints added in 520.1 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 43 through 91 removed outlier: 3.569A pdb=" N ALA A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 152 through 196 removed outlier: 3.561A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 202 through 234 removed outlier: 3.894A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.702A pdb=" N ILE A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 91 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.580A pdb=" N ALA B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 152 through 193 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 204 through 223 Processing helix chain 'B' and resid 223 through 235 removed outlier: 3.713A pdb=" N ALA B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Processing helix chain 'B' and resid 269 through 297 323 hydrogen bonds defined for protein. 969 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: 0.87 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 623 1.31 - 1.44: 1184 1.44 - 1.56: 2381 1.56 - 1.69: 3 1.69 - 1.81: 26 Bond restraints: 4217 Sorted by residual: bond pdb=" CA ILE B 264 " pdb=" C ILE B 264 " ideal model delta sigma weight residual 1.530 1.584 -0.053 1.12e-02 7.97e+03 2.27e+01 bond pdb=" C31 PEV A 401 " pdb=" O2 PEV A 401 " ideal model delta sigma weight residual 1.330 1.409 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C11 PEV A 401 " pdb=" O3 PEV A 401 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" CA THR A 251 " pdb=" C THR A 251 " ideal model delta sigma weight residual 1.525 1.488 0.037 1.40e-02 5.10e+03 7.01e+00 bond pdb=" N THR A 251 " pdb=" CA THR A 251 " ideal model delta sigma weight residual 1.461 1.431 0.031 1.49e-02 4.50e+03 4.26e+00 ... (remaining 4212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 5583 3.27 - 6.55: 121 6.55 - 9.82: 12 9.82 - 13.09: 4 13.09 - 16.36: 1 Bond angle restraints: 5721 Sorted by residual: angle pdb=" C ILE B 264 " pdb=" CA ILE B 264 " pdb=" CB ILE B 264 " ideal model delta sigma weight residual 112.19 102.19 10.00 1.15e+00 7.56e-01 7.56e+01 angle pdb=" N GLU B 263 " pdb=" CA GLU B 263 " pdb=" C GLU B 263 " ideal model delta sigma weight residual 111.17 122.10 -10.93 1.41e+00 5.03e-01 6.01e+01 angle pdb=" C GLU B 263 " pdb=" CA GLU B 263 " pdb=" CB GLU B 263 " ideal model delta sigma weight residual 112.06 101.34 10.72 1.57e+00 4.06e-01 4.66e+01 angle pdb=" N TRP A 199 " pdb=" CA TRP A 199 " pdb=" C TRP A 199 " ideal model delta sigma weight residual 108.52 118.91 -10.39 1.63e+00 3.76e-01 4.06e+01 angle pdb=" O3P PEV A 401 " pdb=" P PEV A 401 " pdb=" O4P PEV A 401 " ideal model delta sigma weight residual 93.57 109.93 -16.36 3.00e+00 1.11e-01 2.98e+01 ... (remaining 5716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 2302 27.26 - 54.53: 105 54.53 - 81.79: 8 81.79 - 109.05: 0 109.05 - 136.32: 1 Dihedral angle restraints: 2416 sinusoidal: 947 harmonic: 1469 Sorted by residual: dihedral pdb=" CA GLN B 122 " pdb=" C GLN B 122 " pdb=" N GLU B 123 " pdb=" CA GLU B 123 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" C3 PEV A 401 " pdb=" C1 PEV A 401 " pdb=" C2 PEV A 401 " pdb=" O3P PEV A 401 " ideal model delta sinusoidal sigma weight residual 292.80 156.48 136.32 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CA LEU B 68 " pdb=" C LEU B 68 " pdb=" N GLU B 69 " pdb=" CA GLU B 69 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 2413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 591 0.089 - 0.178: 68 0.178 - 0.266: 5 0.266 - 0.355: 1 0.355 - 0.444: 2 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA THR A 251 " pdb=" N THR A 251 " pdb=" C THR A 251 " pdb=" CB THR A 251 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ILE B 264 " pdb=" N ILE B 264 " pdb=" C ILE B 264 " pdb=" CB ILE B 264 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 664 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 119 " 0.057 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO A 120 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 115 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 116 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 196 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C PHE A 196 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE A 196 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 197 " -0.013 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 1450 2.88 - 3.44: 5034 3.44 - 4.01: 7273 4.01 - 4.57: 10264 4.57 - 5.14: 14449 Nonbonded interactions: 38470 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR A 266 " model vdw 2.309 3.040 nonbonded pdb=" O PRO A 116 " pdb=" NZ LYS B 84 " model vdw 2.335 3.120 nonbonded pdb=" NZ LYS A 84 " pdb=" O PRO B 116 " model vdw 2.349 3.120 nonbonded pdb=" C ILE A 264 " pdb=" OE1 GLU A 265 " model vdw 2.376 3.270 nonbonded pdb=" OE1 GLN A 231 " pdb=" OG SER A 241 " model vdw 2.414 3.040 ... (remaining 38465 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 297) selection = chain 'B' } 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: 0.390 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 4217 Z= 0.348 Angle : 1.125 16.364 5721 Z= 0.634 Chirality : 0.059 0.444 667 Planarity : 0.008 0.088 685 Dihedral : 14.378 136.317 1475 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.23 % Allowed : 2.06 % Favored : 97.71 % 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: 2.27 (0.35), residues: 513 helix: 2.42 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -1.75 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 127 HIS 0.006 0.001 HIS B 91 PHE 0.039 0.003 PHE A 276 TYR 0.016 0.002 TYR B 284 ARG 0.003 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8274 (tttt) cc_final: 0.7237 (ttmm) REVERT: A 77 LYS cc_start: 0.9185 (mttm) cc_final: 0.8964 (mtpt) REVERT: A 82 GLN cc_start: 0.8363 (pt0) cc_final: 0.7630 (pp30) REVERT: A 86 ASP cc_start: 0.8291 (m-30) cc_final: 0.7641 (m-30) REVERT: A 104 LYS cc_start: 0.9424 (ttpp) cc_final: 0.9104 (ttpp) REVERT: A 105 GLN cc_start: 0.8742 (mt0) cc_final: 0.8438 (pt0) REVERT: A 195 MET cc_start: 0.8544 (tmm) cc_final: 0.7513 (tmm) REVERT: A 268 ASP cc_start: 0.7318 (t70) cc_final: 0.6974 (t0) REVERT: B 66 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8149 (ttmm) REVERT: B 120 PRO cc_start: 0.8391 (Cg_endo) cc_final: 0.7369 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1639 time to fit residues: 45.4252 Evaluate side-chains 193 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4217 Z= 0.243 Angle : 0.758 6.830 5721 Z= 0.398 Chirality : 0.045 0.178 667 Planarity : 0.005 0.041 685 Dihedral : 10.427 139.036 586 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.43 % Allowed : 15.79 % Favored : 80.78 % 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: 2.69 (0.36), residues: 513 helix: 2.64 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.49 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 199 HIS 0.006 0.002 HIS A 232 PHE 0.022 0.002 PHE A 158 TYR 0.017 0.002 TYR B 266 ARG 0.002 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8324 (tttt) cc_final: 0.7520 (ttmm) REVERT: A 79 ARG cc_start: 0.8385 (tmt-80) cc_final: 0.7869 (tpt90) REVERT: A 82 GLN cc_start: 0.8420 (pt0) cc_final: 0.7822 (pp30) REVERT: A 86 ASP cc_start: 0.8177 (m-30) cc_final: 0.7836 (m-30) REVERT: A 95 GLN cc_start: 0.8579 (tp40) cc_final: 0.7865 (tp40) REVERT: A 101 ASP cc_start: 0.8413 (t0) cc_final: 0.8153 (t0) REVERT: A 104 LYS cc_start: 0.9431 (ttpp) cc_final: 0.9086 (ttpp) REVERT: A 180 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7769 (tp40) REVERT: A 263 GLU cc_start: 0.7586 (tt0) cc_final: 0.7301 (tt0) REVERT: A 268 ASP cc_start: 0.7280 (t70) cc_final: 0.6923 (t70) REVERT: B 45 LYS cc_start: 0.8088 (mtmm) cc_final: 0.7826 (mmtt) REVERT: B 50 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8280 (tt) REVERT: B 66 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8053 (ttmt) REVERT: B 122 GLN cc_start: 0.7213 (mp-120) cc_final: 0.6570 (mp10) REVERT: B 222 PHE cc_start: 0.7445 (m-80) cc_final: 0.7142 (m-10) outliers start: 15 outliers final: 6 residues processed: 218 average time/residue: 0.1697 time to fit residues: 45.2825 Evaluate side-chains 207 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 36 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4217 Z= 0.255 Angle : 0.787 11.206 5721 Z= 0.398 Chirality : 0.044 0.189 667 Planarity : 0.005 0.048 685 Dihedral : 10.467 135.587 586 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.12 % Allowed : 21.05 % Favored : 74.83 % 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: 2.49 (0.36), residues: 513 helix: 2.44 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -1.36 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 295 HIS 0.006 0.001 HIS A 232 PHE 0.022 0.002 PHE A 158 TYR 0.021 0.002 TYR A 57 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8251 (tttt) cc_final: 0.7606 (ttmm) REVERT: A 82 GLN cc_start: 0.8405 (pt0) cc_final: 0.7533 (pp30) REVERT: A 86 ASP cc_start: 0.8239 (m-30) cc_final: 0.7669 (m-30) REVERT: A 101 ASP cc_start: 0.8496 (t0) cc_final: 0.8272 (t0) REVERT: A 104 LYS cc_start: 0.9443 (ttpp) cc_final: 0.9121 (ttpp) REVERT: A 268 ASP cc_start: 0.7374 (t70) cc_final: 0.6858 (t70) REVERT: B 43 LYS cc_start: 0.7398 (tptt) cc_final: 0.6991 (tptt) REVERT: B 48 LEU cc_start: 0.9022 (mt) cc_final: 0.8739 (mt) REVERT: B 66 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8215 (ttmm) REVERT: B 240 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7653 (mt-10) REVERT: B 295 TRP cc_start: 0.7572 (OUTLIER) cc_final: 0.6803 (m100) outliers start: 18 outliers final: 10 residues processed: 210 average time/residue: 0.1710 time to fit residues: 43.5477 Evaluate side-chains 194 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 115 ASN B 122 GLN B 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4217 Z= 0.244 Angle : 0.807 10.172 5721 Z= 0.410 Chirality : 0.044 0.170 667 Planarity : 0.004 0.040 685 Dihedral : 10.432 132.951 586 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.12 % Allowed : 23.34 % Favored : 72.54 % 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: 2.42 (0.36), residues: 513 helix: 2.41 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -1.48 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 295 HIS 0.001 0.000 HIS B 151 PHE 0.019 0.001 PHE A 217 TYR 0.022 0.002 TYR A 162 ARG 0.006 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8317 (tttt) cc_final: 0.7551 (ttmm) REVERT: A 82 GLN cc_start: 0.8469 (pt0) cc_final: 0.7611 (pp30) REVERT: A 83 GLU cc_start: 0.8234 (tp30) cc_final: 0.7811 (tp30) REVERT: A 86 ASP cc_start: 0.8249 (m-30) cc_final: 0.7691 (m-30) REVERT: A 104 LYS cc_start: 0.9443 (ttpp) cc_final: 0.9177 (ttpp) REVERT: B 45 LYS cc_start: 0.8122 (pttp) cc_final: 0.7901 (mmtt) REVERT: B 48 LEU cc_start: 0.8994 (mt) cc_final: 0.8728 (mt) REVERT: B 51 PHE cc_start: 0.9280 (t80) cc_final: 0.9033 (t80) REVERT: B 58 LEU cc_start: 0.8867 (mt) cc_final: 0.8536 (mt) REVERT: B 66 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8229 (ttmm) REVERT: B 86 ASP cc_start: 0.8699 (p0) cc_final: 0.8413 (p0) REVERT: B 195 MET cc_start: 0.7312 (mmm) cc_final: 0.6967 (mpp) REVERT: B 291 MET cc_start: 0.8148 (tmm) cc_final: 0.7806 (mmp) outliers start: 18 outliers final: 11 residues processed: 213 average time/residue: 0.1703 time to fit residues: 44.0830 Evaluate side-chains 213 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.0060 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4217 Z= 0.263 Angle : 0.829 10.390 5721 Z= 0.418 Chirality : 0.044 0.164 667 Planarity : 0.004 0.044 685 Dihedral : 10.436 130.911 586 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.66 % Allowed : 27.92 % Favored : 68.42 % 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: 2.33 (0.36), residues: 513 helix: 2.32 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -1.42 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 295 HIS 0.001 0.001 HIS B 151 PHE 0.017 0.001 PHE A 217 TYR 0.023 0.002 TYR A 162 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8317 (tttt) cc_final: 0.7530 (ttmm) REVERT: A 82 GLN cc_start: 0.8461 (pt0) cc_final: 0.7700 (pp30) REVERT: A 86 ASP cc_start: 0.8274 (m-30) cc_final: 0.7877 (m-30) REVERT: A 104 LYS cc_start: 0.9437 (ttpp) cc_final: 0.9170 (ttpp) REVERT: A 174 LEU cc_start: 0.8755 (tp) cc_final: 0.8430 (tp) REVERT: B 43 LYS cc_start: 0.7338 (tptt) cc_final: 0.7133 (tptt) REVERT: B 48 LEU cc_start: 0.9029 (mt) cc_final: 0.8772 (mt) REVERT: B 51 PHE cc_start: 0.9261 (t80) cc_final: 0.9022 (t80) REVERT: B 58 LEU cc_start: 0.8923 (mt) cc_final: 0.8608 (mt) REVERT: B 66 LYS cc_start: 0.8935 (ttpt) cc_final: 0.8667 (ttpp) REVERT: B 70 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8090 (mm-40) REVERT: B 86 ASP cc_start: 0.8618 (p0) cc_final: 0.8219 (p0) REVERT: B 100 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8118 (tp30) REVERT: B 104 LYS cc_start: 0.9253 (ttmm) cc_final: 0.8920 (mtmm) outliers start: 16 outliers final: 11 residues processed: 213 average time/residue: 0.1696 time to fit residues: 43.9179 Evaluate side-chains 196 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4217 Z= 0.258 Angle : 0.896 11.864 5721 Z= 0.437 Chirality : 0.045 0.166 667 Planarity : 0.004 0.037 685 Dihedral : 10.328 128.574 586 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.97 % Allowed : 30.21 % Favored : 66.82 % 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: 2.06 (0.36), residues: 513 helix: 2.14 (0.24), residues: 399 sheet: None (None), residues: 0 loop : -1.54 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 295 HIS 0.001 0.001 HIS A 91 PHE 0.021 0.001 PHE B 158 TYR 0.020 0.002 TYR A 162 ARG 0.009 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8310 (tttt) cc_final: 0.7515 (ttmm) REVERT: A 82 GLN cc_start: 0.8524 (pt0) cc_final: 0.7726 (pp30) REVERT: A 86 ASP cc_start: 0.8312 (m-30) cc_final: 0.7930 (m-30) REVERT: B 51 PHE cc_start: 0.9233 (t80) cc_final: 0.9030 (t80) REVERT: B 58 LEU cc_start: 0.8940 (mt) cc_final: 0.8584 (mp) REVERT: B 66 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8291 (ttpt) REVERT: B 70 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8164 (mm-40) REVERT: B 86 ASP cc_start: 0.8575 (p0) cc_final: 0.8137 (p0) REVERT: B 100 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8062 (tp30) REVERT: B 104 LYS cc_start: 0.9207 (ttmm) cc_final: 0.9001 (mtmm) REVERT: B 291 MET cc_start: 0.8092 (tmm) cc_final: 0.7565 (mmp) outliers start: 13 outliers final: 10 residues processed: 196 average time/residue: 0.1818 time to fit residues: 43.1517 Evaluate side-chains 192 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.0000 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4217 Z= 0.264 Angle : 0.872 10.721 5721 Z= 0.433 Chirality : 0.046 0.213 667 Planarity : 0.004 0.041 685 Dihedral : 10.165 126.569 586 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.97 % Allowed : 29.29 % Favored : 67.73 % 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: 2.01 (0.36), residues: 513 helix: 2.13 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.60 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 295 HIS 0.002 0.000 HIS B 151 PHE 0.023 0.001 PHE B 158 TYR 0.018 0.002 TYR B 57 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7593 (mmtm) REVERT: A 66 LYS cc_start: 0.8352 (tttt) cc_final: 0.7608 (ttmm) REVERT: A 82 GLN cc_start: 0.8548 (pt0) cc_final: 0.7899 (pp30) REVERT: A 86 ASP cc_start: 0.8228 (m-30) cc_final: 0.7828 (m-30) REVERT: B 48 LEU cc_start: 0.9037 (mt) cc_final: 0.8799 (mt) REVERT: B 51 PHE cc_start: 0.9239 (t80) cc_final: 0.9013 (t80) REVERT: B 58 LEU cc_start: 0.8915 (mt) cc_final: 0.8568 (mp) REVERT: B 66 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8636 (ttpp) REVERT: B 70 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8179 (mm-40) REVERT: B 104 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8990 (mtmm) REVERT: B 291 MET cc_start: 0.8215 (tmm) cc_final: 0.7675 (mmp) outliers start: 13 outliers final: 11 residues processed: 193 average time/residue: 0.1841 time to fit residues: 43.0875 Evaluate side-chains 197 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4217 Z= 0.255 Angle : 0.876 10.314 5721 Z= 0.438 Chirality : 0.046 0.171 667 Planarity : 0.004 0.051 685 Dihedral : 10.111 123.946 586 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.75 % Allowed : 29.98 % Favored : 67.28 % 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: 2.00 (0.36), residues: 513 helix: 2.12 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.61 (0.54), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 295 HIS 0.002 0.001 HIS B 232 PHE 0.023 0.001 PHE A 158 TYR 0.018 0.002 TYR B 57 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7581 (mmtm) REVERT: A 66 LYS cc_start: 0.8349 (tttt) cc_final: 0.7633 (ttmm) REVERT: A 82 GLN cc_start: 0.8518 (pt0) cc_final: 0.7882 (pp30) REVERT: A 86 ASP cc_start: 0.8271 (m-30) cc_final: 0.7917 (m-30) REVERT: B 48 LEU cc_start: 0.9035 (mt) cc_final: 0.8738 (mt) REVERT: B 70 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8178 (mm-40) REVERT: B 282 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8233 (mt) REVERT: B 291 MET cc_start: 0.8187 (tmm) cc_final: 0.7651 (mmp) outliers start: 12 outliers final: 9 residues processed: 186 average time/residue: 0.1874 time to fit residues: 41.9371 Evaluate side-chains 186 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4217 Z= 0.272 Angle : 0.878 10.043 5721 Z= 0.442 Chirality : 0.046 0.176 667 Planarity : 0.004 0.043 685 Dihedral : 10.014 121.594 586 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.43 % Allowed : 30.43 % Favored : 66.13 % 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: 1.99 (0.36), residues: 513 helix: 2.13 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.68 (0.53), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 199 HIS 0.002 0.001 HIS B 151 PHE 0.028 0.002 PHE B 158 TYR 0.020 0.003 TYR A 57 ARG 0.004 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7641 (mmtm) REVERT: A 66 LYS cc_start: 0.8371 (tttt) cc_final: 0.7639 (ttmm) REVERT: A 76 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8895 (mm110) REVERT: A 82 GLN cc_start: 0.8540 (pt0) cc_final: 0.7899 (pp30) REVERT: A 83 GLU cc_start: 0.8163 (tp30) cc_final: 0.7887 (tp30) REVERT: A 86 ASP cc_start: 0.8274 (m-30) cc_final: 0.7915 (m-30) REVERT: A 174 LEU cc_start: 0.8801 (tp) cc_final: 0.8550 (tp) REVERT: A 282 LEU cc_start: 0.8861 (mt) cc_final: 0.8623 (mt) REVERT: B 48 LEU cc_start: 0.9034 (mt) cc_final: 0.8735 (mt) REVERT: B 70 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8226 (mm-40) REVERT: B 105 GLN cc_start: 0.8418 (mp10) cc_final: 0.8125 (mp10) REVERT: B 282 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8295 (mt) REVERT: B 291 MET cc_start: 0.8161 (tmm) cc_final: 0.7812 (mmp) outliers start: 15 outliers final: 10 residues processed: 182 average time/residue: 0.1732 time to fit residues: 38.5390 Evaluate side-chains 179 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.0050 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4217 Z= 0.244 Angle : 0.917 12.040 5721 Z= 0.456 Chirality : 0.046 0.180 667 Planarity : 0.005 0.048 685 Dihedral : 9.808 116.525 586 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.83 % Allowed : 32.04 % Favored : 66.13 % 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: 2.00 (0.37), residues: 513 helix: 2.13 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.66 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 295 HIS 0.001 0.001 HIS B 151 PHE 0.026 0.001 PHE B 158 TYR 0.018 0.002 TYR B 57 ARG 0.014 0.001 ARG A 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8354 (tttt) cc_final: 0.7652 (ttmt) REVERT: A 82 GLN cc_start: 0.8509 (pt0) cc_final: 0.7817 (pp30) REVERT: A 86 ASP cc_start: 0.8230 (m-30) cc_final: 0.7594 (m-30) REVERT: A 198 LYS cc_start: 0.8359 (pptt) cc_final: 0.8067 (mmtt) REVERT: A 241 SER cc_start: 0.8499 (m) cc_final: 0.8016 (t) REVERT: B 48 LEU cc_start: 0.9004 (mt) cc_final: 0.8776 (mt) REVERT: B 66 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8085 (ttmt) REVERT: B 291 MET cc_start: 0.7988 (tmm) cc_final: 0.7729 (mmp) outliers start: 8 outliers final: 7 residues processed: 184 average time/residue: 0.1866 time to fit residues: 41.6927 Evaluate side-chains 190 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.145233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110117 restraints weight = 7432.818| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 4.16 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4217 Z= 0.266 Angle : 0.950 11.805 5721 Z= 0.478 Chirality : 0.047 0.191 667 Planarity : 0.004 0.039 685 Dihedral : 9.765 114.188 586 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.60 % Allowed : 34.10 % Favored : 64.30 % 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: 1.90 (0.36), residues: 513 helix: 2.05 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.67 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 295 HIS 0.002 0.001 HIS B 151 PHE 0.031 0.002 PHE B 158 TYR 0.018 0.002 TYR A 162 ARG 0.001 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1518.58 seconds wall clock time: 28 minutes 11.23 seconds (1691.23 seconds total)