Starting phenix.real_space_refine on Sat May 10 00:27:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dki_27489/05_2025/8dki_27489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dki_27489/05_2025/8dki_27489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dki_27489/05_2025/8dki_27489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dki_27489/05_2025/8dki_27489.map" model { file = "/net/cci-nas-00/data/ceres_data/8dki_27489/05_2025/8dki_27489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dki_27489/05_2025/8dki_27489_neut.cif" } resolution = 3.32 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= 0.004 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2858 2.51 5 N 703 2.21 5 O 789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4365 Number of models: 1 Model: "" Number of chains: 3 Chain: "P" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2679 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 871 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 3.32, per 1000 atoms: 0.76 Number of scatterers: 4365 At special positions: 0 Unit cell: (78.492, 64.988, 114.784, 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 15 16.00 O 789 8.00 N 703 7.00 C 2858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 487.6 milliseconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1018 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 7 sheets defined 38.4% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'P' and resid 120 through 141 Processing helix chain 'P' and resid 141 through 150 removed outlier: 4.618A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 180 Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 Processing helix chain 'P' and resid 234 through 257 removed outlier: 3.662A pdb=" N VAL P 257 " --> pdb=" O ILE P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 279 removed outlier: 3.586A pdb=" N PHE P 265 " --> pdb=" O THR P 261 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE P 269 " --> pdb=" O PHE P 265 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER P 270 " --> pdb=" O LEU P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 292 removed outlier: 3.748A pdb=" N TYR P 291 " --> pdb=" O MET P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 323 removed outlier: 3.685A pdb=" N VAL P 302 " --> pdb=" O SER P 298 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR P 321 " --> pdb=" O PHE P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 325 through 330 Processing helix chain 'P' and resid 332 through 355 removed outlier: 3.627A pdb=" N PHE P 336 " --> pdb=" O ASP P 332 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.002A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.762A pdb=" N THR A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 26 through 27 removed outlier: 3.831A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 31 through 35 removed outlier: 3.934A pdb=" N VAL P 32 " --> pdb=" O ARG P 114 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.582A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.648A pdb=" N ILE B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.426A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.351A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 639 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: 1.12 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 885 1.33 - 1.45: 1158 1.45 - 1.57: 2420 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4485 Sorted by residual: bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.19e+01 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.51e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.34e-02 5.57e+03 6.21e+00 bond pdb=" C PHE P 317 " pdb=" O PHE P 317 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.19e-02 7.06e+03 5.45e+00 bond pdb=" C MET P 316 " pdb=" O MET P 316 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.26e-02 6.30e+03 4.55e+00 ... (remaining 4480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 5902 1.50 - 2.99: 161 2.99 - 4.49: 44 4.49 - 5.99: 8 5.99 - 7.48: 2 Bond angle restraints: 6117 Sorted by residual: angle pdb=" C PRO A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N MET P 316 " pdb=" CA MET P 316 " pdb=" C MET P 316 " ideal model delta sigma weight residual 111.82 108.02 3.80 1.16e+00 7.43e-01 1.08e+01 angle pdb=" CA THR P 261 " pdb=" C THR P 261 " pdb=" O THR P 261 " ideal model delta sigma weight residual 121.87 118.14 3.73 1.16e+00 7.43e-01 1.03e+01 angle pdb=" N ILE P 69 " pdb=" CA ILE P 69 " pdb=" C ILE P 69 " ideal model delta sigma weight residual 111.48 108.48 3.00 9.40e-01 1.13e+00 1.02e+01 angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 113.18 119.11 -5.93 2.37e+00 1.78e-01 6.27e+00 ... (remaining 6112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2333 17.95 - 35.90: 207 35.90 - 53.84: 30 53.84 - 71.79: 3 71.79 - 89.74: 5 Dihedral angle restraints: 2578 sinusoidal: 984 harmonic: 1594 Sorted by residual: dihedral pdb=" CA ARG P 47 " pdb=" C ARG P 47 " pdb=" N PRO P 48 " pdb=" CA PRO P 48 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ARG P 151 " pdb=" C ARG P 151 " pdb=" N ARG P 152 " pdb=" CA ARG P 152 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PRO A 41 " pdb=" C PRO A 41 " pdb=" N GLU A 42 " pdb=" CA GLU A 42 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 582 0.059 - 0.119: 97 0.119 - 0.178: 11 0.178 - 0.238: 1 0.238 - 0.297: 1 Chirality restraints: 692 Sorted by residual: chirality pdb=" CA LEU P 318 " pdb=" N LEU P 318 " pdb=" C LEU P 318 " pdb=" CB LEU P 318 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PHE P 317 " pdb=" N PHE P 317 " pdb=" C PHE P 317 " pdb=" CB PHE P 317 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL P 279 " pdb=" CA VAL P 279 " pdb=" CG1 VAL P 279 " pdb=" CG2 VAL P 279 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 689 not shown) Planarity restraints: 765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 182 " 0.015 2.00e-02 2.50e+03 1.32e-02 4.35e+00 pdb=" CG TRP P 182 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP P 182 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP P 182 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 182 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 182 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 182 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 182 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR P 143 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO P 144 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO P 144 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO P 144 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 341 " -0.014 2.00e-02 2.50e+03 1.27e-02 2.80e+00 pdb=" CG PHE P 341 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE P 341 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE P 341 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE P 341 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE P 341 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE P 341 " -0.001 2.00e-02 2.50e+03 ... (remaining 762 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 390 2.74 - 3.28: 4352 3.28 - 3.82: 7394 3.82 - 4.36: 8374 4.36 - 4.90: 14840 Nonbonded interactions: 35350 Sorted by model distance: nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR P 281 " pdb=" OD2 ASP P 305 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 7 " pdb=" OG SER A 21 " model vdw 2.256 3.040 nonbonded pdb=" NE2 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.292 3.120 nonbonded pdb=" O PRO P 49 " pdb=" OH TYR A 100 " model vdw 2.298 3.040 ... (remaining 35345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.120 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.003 0.039 4487 Z= 0.179 Angle : 0.641 7.482 6121 Z= 0.347 Chirality : 0.046 0.297 692 Planarity : 0.004 0.047 765 Dihedral : 13.794 89.741 1554 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.21 % Allowed : 0.41 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.37), residues: 546 helix: 1.17 (0.38), residues: 199 sheet: -1.09 (0.44), residues: 150 loop : -1.41 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.029 0.002 PHE P 341 TYR 0.012 0.001 TYR P 134 ARG 0.008 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.13558 ( 225) hydrogen bonds : angle 6.44197 ( 639) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.16547 ( 4) covalent geometry : bond 0.00341 ( 4485) covalent geometry : angle 0.64088 ( 6117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.456 Fit side-chains REVERT: P 140 ILE cc_start: 0.8683 (tt) cc_final: 0.8455 (tt) REVERT: P 317 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6764 (t80) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1746 time to fit residues: 22.1895 Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 317 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 96 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118271 restraints weight = 5206.275| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.05 r_work: 0.3168 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4487 Z= 0.209 Angle : 0.647 8.911 6121 Z= 0.328 Chirality : 0.045 0.152 692 Planarity : 0.005 0.048 765 Dihedral : 5.238 50.969 597 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.66 % Allowed : 9.54 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.38), residues: 546 helix: 1.62 (0.38), residues: 201 sheet: -1.16 (0.43), residues: 150 loop : -1.47 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP P 182 HIS 0.003 0.001 HIS B 55 PHE 0.013 0.001 PHE P 240 TYR 0.020 0.002 TYR P 134 ARG 0.004 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 225) hydrogen bonds : angle 4.88657 ( 639) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.42276 ( 4) covalent geometry : bond 0.00502 ( 4485) covalent geometry : angle 0.64731 ( 6117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.518 Fit side-chains REVERT: P 140 ILE cc_start: 0.8736 (tt) cc_final: 0.8520 (tt) REVERT: P 356 LEU cc_start: 0.8636 (mp) cc_final: 0.8345 (mp) REVERT: A 31 ASN cc_start: 0.8888 (m-40) cc_final: 0.8601 (m-40) outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.1605 time to fit residues: 19.6303 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 264 GLN A 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119471 restraints weight = 5370.538| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.34 r_work: 0.3199 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4487 Z= 0.145 Angle : 0.589 7.662 6121 Z= 0.301 Chirality : 0.043 0.144 692 Planarity : 0.004 0.044 765 Dihedral : 4.592 22.894 595 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.07 % Allowed : 12.45 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.38), residues: 546 helix: 1.79 (0.38), residues: 200 sheet: -1.09 (0.43), residues: 150 loop : -1.41 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.012 0.001 PHE P 87 TYR 0.017 0.002 TYR P 134 ARG 0.003 0.000 ARG P 152 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 225) hydrogen bonds : angle 4.69036 ( 639) SS BOND : bond 0.00196 ( 2) SS BOND : angle 0.24261 ( 4) covalent geometry : bond 0.00339 ( 4485) covalent geometry : angle 0.58932 ( 6117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.508 Fit side-chains REVERT: P 140 ILE cc_start: 0.8639 (tt) cc_final: 0.8422 (tt) REVERT: P 341 PHE cc_start: 0.8276 (t80) cc_final: 0.8070 (t80) REVERT: P 356 LEU cc_start: 0.8618 (mp) cc_final: 0.8323 (mp) REVERT: A 31 ASN cc_start: 0.8851 (m-40) cc_final: 0.8570 (m-40) REVERT: A 55 GLU cc_start: 0.7628 (mp0) cc_final: 0.7378 (mp0) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1539 time to fit residues: 20.2861 Evaluate side-chains 94 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.154122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119065 restraints weight = 5423.513| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.37 r_work: 0.3189 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4487 Z= 0.153 Angle : 0.587 7.145 6121 Z= 0.299 Chirality : 0.044 0.145 692 Planarity : 0.004 0.043 765 Dihedral : 4.543 22.796 595 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.90 % Allowed : 13.90 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.38), residues: 546 helix: 1.82 (0.38), residues: 200 sheet: -0.91 (0.46), residues: 141 loop : -1.46 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 PHE 0.017 0.001 PHE A 69 TYR 0.016 0.001 TYR P 134 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 225) hydrogen bonds : angle 4.60112 ( 639) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.24369 ( 4) covalent geometry : bond 0.00361 ( 4485) covalent geometry : angle 0.58713 ( 6117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.522 Fit side-chains REVERT: P 356 LEU cc_start: 0.8630 (mp) cc_final: 0.8309 (mp) REVERT: A 55 GLU cc_start: 0.7545 (mp0) cc_final: 0.7281 (mp0) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 0.1784 time to fit residues: 21.7932 Evaluate side-chains 94 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 127 ASN P 189 GLN A 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118903 restraints weight = 5479.826| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.36 r_work: 0.3214 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4487 Z= 0.155 Angle : 0.581 6.848 6121 Z= 0.297 Chirality : 0.043 0.145 692 Planarity : 0.004 0.042 765 Dihedral : 4.534 22.766 595 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.70 % Allowed : 15.77 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.38), residues: 546 helix: 1.80 (0.38), residues: 200 sheet: -0.92 (0.46), residues: 142 loop : -1.48 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 PHE 0.017 0.001 PHE A 69 TYR 0.015 0.001 TYR P 185 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 225) hydrogen bonds : angle 4.54763 ( 639) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.21845 ( 4) covalent geometry : bond 0.00366 ( 4485) covalent geometry : angle 0.58164 ( 6117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.453 Fit side-chains REVERT: P 356 LEU cc_start: 0.8656 (mp) cc_final: 0.8379 (mp) REVERT: A 55 GLU cc_start: 0.7512 (mp0) cc_final: 0.7239 (mp0) outliers start: 13 outliers final: 12 residues processed: 93 average time/residue: 0.1450 time to fit residues: 17.4877 Evaluate side-chains 90 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.152052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117194 restraints weight = 5441.580| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.36 r_work: 0.3168 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4487 Z= 0.188 Angle : 0.603 7.125 6121 Z= 0.308 Chirality : 0.044 0.147 692 Planarity : 0.004 0.042 765 Dihedral : 4.634 23.136 595 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.32 % Allowed : 16.80 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.37), residues: 546 helix: 1.51 (0.37), residues: 206 sheet: -0.90 (0.46), residues: 142 loop : -1.57 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 PHE 0.019 0.001 PHE A 69 TYR 0.015 0.002 TYR P 134 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 225) hydrogen bonds : angle 4.60158 ( 639) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.31593 ( 4) covalent geometry : bond 0.00450 ( 4485) covalent geometry : angle 0.60351 ( 6117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.486 Fit side-chains REVERT: P 148 MET cc_start: 0.8364 (ttp) cc_final: 0.7760 (ttp) REVERT: P 356 LEU cc_start: 0.8693 (mp) cc_final: 0.8379 (mp) REVERT: A 55 GLU cc_start: 0.7592 (mp0) cc_final: 0.7320 (mp0) outliers start: 16 outliers final: 15 residues processed: 95 average time/residue: 0.1463 time to fit residues: 18.1511 Evaluate side-chains 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.152712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117820 restraints weight = 5478.859| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.37 r_work: 0.3171 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4487 Z= 0.176 Angle : 0.599 7.401 6121 Z= 0.305 Chirality : 0.044 0.146 692 Planarity : 0.004 0.041 765 Dihedral : 4.607 22.940 595 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.73 % Allowed : 16.18 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.37), residues: 546 helix: 1.52 (0.37), residues: 206 sheet: -0.92 (0.46), residues: 142 loop : -1.58 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 PHE 0.016 0.001 PHE A 69 TYR 0.015 0.002 TYR P 134 ARG 0.006 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 225) hydrogen bonds : angle 4.57951 ( 639) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.28361 ( 4) covalent geometry : bond 0.00420 ( 4485) covalent geometry : angle 0.59911 ( 6117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.550 Fit side-chains REVERT: P 148 MET cc_start: 0.8238 (ttp) cc_final: 0.7624 (ttp) REVERT: P 185 TYR cc_start: 0.8137 (t80) cc_final: 0.7569 (t80) REVERT: P 356 LEU cc_start: 0.8693 (mp) cc_final: 0.8365 (mp) REVERT: A 55 GLU cc_start: 0.7584 (mp0) cc_final: 0.7300 (mp0) outliers start: 18 outliers final: 16 residues processed: 99 average time/residue: 0.1385 time to fit residues: 17.9440 Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120134 restraints weight = 5441.829| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.39 r_work: 0.3225 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4487 Z= 0.137 Angle : 0.581 7.749 6121 Z= 0.296 Chirality : 0.043 0.142 692 Planarity : 0.004 0.040 765 Dihedral : 4.494 22.440 595 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.53 % Allowed : 16.60 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.38), residues: 546 helix: 1.61 (0.37), residues: 206 sheet: -0.89 (0.46), residues: 141 loop : -1.51 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 182 HIS 0.001 0.000 HIS P 211 PHE 0.022 0.001 PHE A 69 TYR 0.013 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 225) hydrogen bonds : angle 4.48407 ( 639) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.18134 ( 4) covalent geometry : bond 0.00320 ( 4485) covalent geometry : angle 0.58130 ( 6117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.526 Fit side-chains REVERT: P 185 TYR cc_start: 0.8091 (t80) cc_final: 0.7544 (t80) REVERT: P 356 LEU cc_start: 0.8672 (mp) cc_final: 0.8351 (mp) REVERT: A 55 GLU cc_start: 0.7418 (mp0) cc_final: 0.7145 (mp0) outliers start: 17 outliers final: 16 residues processed: 94 average time/residue: 0.1484 time to fit residues: 18.0548 Evaluate side-chains 101 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 4 optimal weight: 0.0050 overall best weight: 0.4732 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.156684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121495 restraints weight = 5460.396| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.41 r_work: 0.3222 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4487 Z= 0.125 Angle : 0.571 8.065 6121 Z= 0.289 Chirality : 0.043 0.142 692 Planarity : 0.004 0.039 765 Dihedral : 4.413 22.064 595 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.11 % Allowed : 16.39 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.38), residues: 546 helix: 1.66 (0.38), residues: 206 sheet: -0.86 (0.47), residues: 140 loop : -1.44 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 182 HIS 0.001 0.000 HIS P 211 PHE 0.018 0.001 PHE A 69 TYR 0.013 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 225) hydrogen bonds : angle 4.35506 ( 639) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.14008 ( 4) covalent geometry : bond 0.00291 ( 4485) covalent geometry : angle 0.57097 ( 6117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.454 Fit side-chains REVERT: P 185 TYR cc_start: 0.8085 (t80) cc_final: 0.7559 (t80) REVERT: P 356 LEU cc_start: 0.8650 (mp) cc_final: 0.8342 (mp) REVERT: A 55 GLU cc_start: 0.7344 (mp0) cc_final: 0.7044 (mp0) outliers start: 15 outliers final: 15 residues processed: 101 average time/residue: 0.1476 time to fit residues: 19.2661 Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.157408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122074 restraints weight = 5391.440| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.42 r_work: 0.3228 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4487 Z= 0.123 Angle : 0.576 8.149 6121 Z= 0.292 Chirality : 0.043 0.140 692 Planarity : 0.004 0.039 765 Dihedral : 4.359 21.877 595 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.11 % Allowed : 17.63 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.38), residues: 546 helix: 1.90 (0.38), residues: 200 sheet: -0.88 (0.47), residues: 141 loop : -1.36 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 182 HIS 0.001 0.000 HIS P 211 PHE 0.019 0.001 PHE P 289 TYR 0.012 0.001 TYR P 134 ARG 0.007 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 225) hydrogen bonds : angle 4.32159 ( 639) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.10406 ( 4) covalent geometry : bond 0.00286 ( 4485) covalent geometry : angle 0.57613 ( 6117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.528 Fit side-chains REVERT: P 174 SER cc_start: 0.8375 (p) cc_final: 0.8083 (p) REVERT: P 185 TYR cc_start: 0.8083 (t80) cc_final: 0.7570 (t80) REVERT: P 356 LEU cc_start: 0.8642 (mp) cc_final: 0.8335 (mp) REVERT: A 55 GLU cc_start: 0.7285 (mp0) cc_final: 0.6998 (mp0) outliers start: 15 outliers final: 15 residues processed: 99 average time/residue: 0.1518 time to fit residues: 19.2982 Evaluate side-chains 103 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 345 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.154872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119310 restraints weight = 5448.349| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.41 r_work: 0.3195 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4487 Z= 0.156 Angle : 0.604 8.110 6121 Z= 0.304 Chirality : 0.044 0.144 692 Planarity : 0.004 0.039 765 Dihedral : 4.446 22.395 595 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.32 % Allowed : 18.26 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.38), residues: 546 helix: 1.65 (0.38), residues: 206 sheet: -0.87 (0.47), residues: 141 loop : -1.44 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 PHE 0.021 0.001 PHE A 69 TYR 0.014 0.001 TYR P 134 ARG 0.008 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 225) hydrogen bonds : angle 4.39161 ( 639) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.23154 ( 4) covalent geometry : bond 0.00373 ( 4485) covalent geometry : angle 0.60380 ( 6117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.68 seconds wall clock time: 43 minutes 46.35 seconds (2626.35 seconds total)