Starting phenix.real_space_refine on Wed Sep 17 04:41:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dki_27489/09_2025/8dki_27489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dki_27489/09_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_27489/09_2025/8dki_27489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dki_27489/09_2025/8dki_27489.map" model { file = "/net/cci-nas-00/data/ceres_data/8dki_27489/09_2025/8dki_27489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dki_27489/09_2025/8dki_27489_neut.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.32, per 1000 atoms: 0.30 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: 0.38 Conformation dependent library (CDL) restraints added in 166.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.13 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: 0.67 Time building geometry restraints manager: 0.52 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: 3.040 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG B 24 TYR 0.012 0.001 TYR P 134 PHE 0.029 0.002 PHE P 341 TRP 0.036 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4485) covalent geometry : angle 0.64088 ( 6117) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.16547 ( 4) hydrogen bonds : bond 0.13558 ( 225) hydrogen bonds : angle 6.44197 ( 639) *********************** 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 : 0.167 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: 0.0835 time to fit residues: 10.6247 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 : 0.154 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.155587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122546 restraints weight = 5207.816| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.11 r_work: 0.3205 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4487 Z= 0.162 Angle : 0.618 8.606 6121 Z= 0.313 Chirality : 0.043 0.148 692 Planarity : 0.004 0.047 765 Dihedral : 5.082 49.986 597 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.24 % Allowed : 9.54 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.38), residues: 546 helix: 1.67 (0.38), residues: 201 sheet: -1.10 (0.43), residues: 150 loop : -1.39 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 24 TYR 0.020 0.001 TYR P 134 PHE 0.014 0.001 PHE P 240 TRP 0.027 0.002 TRP P 182 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 4485) covalent geometry : angle 0.61810 ( 6117) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.36279 ( 4) hydrogen bonds : bond 0.03405 ( 225) hydrogen bonds : angle 4.83319 ( 639) *********************** 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 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.161 Fit side-chains REVERT: P 140 ILE cc_start: 0.8673 (tt) cc_final: 0.8471 (tt) REVERT: P 207 PHE cc_start: 0.7212 (t80) cc_final: 0.7008 (t80) REVERT: P 356 LEU cc_start: 0.8573 (mp) cc_final: 0.8300 (mp) REVERT: A 31 ASN cc_start: 0.8882 (m-40) cc_final: 0.8590 (m-40) outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 0.0703 time to fit residues: 8.8501 Evaluate side-chains 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 12 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.154397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119648 restraints weight = 5414.037| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.36 r_work: 0.3199 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4487 Z= 0.156 Angle : 0.588 7.720 6121 Z= 0.300 Chirality : 0.043 0.146 692 Planarity : 0.004 0.044 765 Dihedral : 4.547 22.906 595 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.49 % Allowed : 11.62 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.38), residues: 546 helix: 1.81 (0.38), residues: 200 sheet: -1.11 (0.43), residues: 150 loop : -1.38 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.017 0.001 TYR P 134 PHE 0.013 0.001 PHE P 176 TRP 0.022 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4485) covalent geometry : angle 0.58848 ( 6117) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.25888 ( 4) hydrogen bonds : bond 0.03190 ( 225) hydrogen bonds : angle 4.67274 ( 639) *********************** 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 104 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.160 Fit side-chains REVERT: P 140 ILE cc_start: 0.8634 (tt) cc_final: 0.8376 (tt) REVERT: P 207 PHE cc_start: 0.7125 (t80) cc_final: 0.6899 (t80) REVERT: P 341 PHE cc_start: 0.8276 (t80) cc_final: 0.8069 (t80) REVERT: P 356 LEU cc_start: 0.8612 (mp) cc_final: 0.8314 (mp) REVERT: A 31 ASN cc_start: 0.8831 (m-40) cc_final: 0.8545 (m-40) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.0666 time to fit residues: 8.4400 Evaluate side-chains 96 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 155 VAL 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 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.153167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118330 restraints weight = 5391.035| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.36 r_work: 0.3184 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4487 Z= 0.170 Angle : 0.594 7.275 6121 Z= 0.302 Chirality : 0.044 0.146 692 Planarity : 0.004 0.042 765 Dihedral : 4.574 23.008 595 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.49 % Allowed : 13.28 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.38), residues: 546 helix: 1.83 (0.38), residues: 200 sheet: -0.97 (0.46), residues: 142 loop : -1.45 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.016 0.002 TYR P 134 PHE 0.017 0.001 PHE A 69 TRP 0.018 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 4485) covalent geometry : angle 0.59378 ( 6117) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.27643 ( 4) hydrogen bonds : bond 0.03137 ( 225) hydrogen bonds : angle 4.61811 ( 639) *********************** 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: 12 poor density : 91 time to evaluate : 0.162 Fit side-chains REVERT: P 140 ILE cc_start: 0.8693 (tt) cc_final: 0.8456 (tt) REVERT: P 207 PHE cc_start: 0.7090 (t80) cc_final: 0.6876 (t80) REVERT: P 341 PHE cc_start: 0.8310 (t80) cc_final: 0.8096 (t80) REVERT: P 356 LEU cc_start: 0.8655 (mp) cc_final: 0.8334 (mp) REVERT: A 55 GLU cc_start: 0.7585 (mp0) cc_final: 0.7342 (mp0) outliers start: 12 outliers final: 11 residues processed: 96 average time/residue: 0.0653 time to fit residues: 8.1315 Evaluate side-chains 94 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 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 93 ASN P 127 ASN P 189 GLN A 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118998 restraints weight = 5423.815| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.33 r_work: 0.3189 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1646 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= 0.155 Angle : 0.582 6.800 6121 Z= 0.297 Chirality : 0.044 0.145 692 Planarity : 0.004 0.042 765 Dihedral : 4.527 22.826 595 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.70 % Allowed : 15.35 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.38), residues: 546 helix: 1.83 (0.38), residues: 200 sheet: -0.93 (0.46), residues: 142 loop : -1.46 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.015 0.001 TYR P 134 PHE 0.013 0.001 PHE A 69 TRP 0.015 0.001 TRP P 182 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4485) covalent geometry : angle 0.58212 ( 6117) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.21702 ( 4) hydrogen bonds : bond 0.03063 ( 225) hydrogen bonds : angle 4.57159 ( 639) *********************** 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 103 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.169 Fit side-chains REVERT: P 180 LEU cc_start: 0.7897 (mt) cc_final: 0.7676 (mt) REVERT: P 207 PHE cc_start: 0.7187 (t80) cc_final: 0.6962 (t80) REVERT: P 356 LEU cc_start: 0.8650 (mp) cc_final: 0.8378 (mp) REVERT: A 55 GLU cc_start: 0.7552 (mp0) cc_final: 0.7320 (mp0) outliers start: 13 outliers final: 13 residues processed: 97 average time/residue: 0.0705 time to fit residues: 8.7011 Evaluate side-chains 97 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 96 GLN P 189 GLN P 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117481 restraints weight = 5524.622| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.37 r_work: 0.3164 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4487 Z= 0.194 Angle : 0.607 7.032 6121 Z= 0.309 Chirality : 0.045 0.147 692 Planarity : 0.004 0.042 765 Dihedral : 4.643 23.157 595 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.11 % Allowed : 15.77 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.37), residues: 546 helix: 1.57 (0.37), residues: 206 sheet: -0.97 (0.46), residues: 142 loop : -1.58 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.016 0.002 TYR P 134 PHE 0.027 0.001 PHE A 69 TRP 0.015 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 4485) covalent geometry : angle 0.60675 ( 6117) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.31813 ( 4) hydrogen bonds : bond 0.03204 ( 225) hydrogen bonds : angle 4.60622 ( 639) *********************** 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 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.175 Fit side-chains REVERT: P 207 PHE cc_start: 0.7172 (t80) cc_final: 0.6966 (t80) REVERT: P 356 LEU cc_start: 0.8710 (mp) cc_final: 0.8402 (mp) REVERT: A 55 GLU cc_start: 0.7621 (mp0) cc_final: 0.7364 (mp0) REVERT: B 61 ARG cc_start: 0.8382 (ttm170) cc_final: 0.7997 (ttm170) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.0679 time to fit residues: 8.0780 Evaluate side-chains 94 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.151858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116595 restraints weight = 5480.653| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.38 r_work: 0.3151 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4487 Z= 0.209 Angle : 0.625 7.308 6121 Z= 0.318 Chirality : 0.045 0.148 692 Planarity : 0.004 0.041 765 Dihedral : 4.739 23.385 595 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.94 % Allowed : 15.35 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.37), residues: 546 helix: 1.53 (0.37), residues: 206 sheet: -0.99 (0.46), residues: 142 loop : -1.63 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 24 TYR 0.016 0.002 TYR P 134 PHE 0.023 0.001 PHE A 69 TRP 0.017 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 4485) covalent geometry : angle 0.62542 ( 6117) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.33732 ( 4) hydrogen bonds : bond 0.03302 ( 225) hydrogen bonds : angle 4.63678 ( 639) *********************** 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 101 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.169 Fit side-chains REVERT: P 207 PHE cc_start: 0.7336 (t80) cc_final: 0.7123 (t80) REVERT: P 356 LEU cc_start: 0.8724 (mp) cc_final: 0.8397 (mp) REVERT: A 55 GLU cc_start: 0.7652 (mp0) cc_final: 0.7388 (mp0) outliers start: 19 outliers final: 18 residues processed: 95 average time/residue: 0.0646 time to fit residues: 8.0009 Evaluate side-chains 95 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 126 ILE 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 42 ASP 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 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.155397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120268 restraints weight = 5491.636| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.40 r_work: 0.3203 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4487 Z= 0.133 Angle : 0.572 7.745 6121 Z= 0.291 Chirality : 0.043 0.142 692 Planarity : 0.004 0.040 765 Dihedral : 4.491 22.733 595 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.53 % Allowed : 15.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.38), residues: 546 helix: 1.61 (0.38), residues: 206 sheet: -0.92 (0.46), residues: 141 loop : -1.44 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.013 0.001 TYR P 134 PHE 0.016 0.001 PHE A 69 TRP 0.011 0.001 TRP P 182 HIS 0.001 0.000 HIS P 211 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4485) covalent geometry : angle 0.57211 ( 6117) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.15785 ( 4) hydrogen bonds : bond 0.02905 ( 225) hydrogen bonds : angle 4.46781 ( 639) *********************** 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 : 0.224 Fit side-chains REVERT: P 207 PHE cc_start: 0.7281 (t80) cc_final: 0.7066 (t80) REVERT: P 356 LEU cc_start: 0.8681 (mp) cc_final: 0.8363 (mp) REVERT: A 55 GLU cc_start: 0.7407 (mp0) cc_final: 0.7152 (mp0) outliers start: 17 outliers final: 17 residues processed: 95 average time/residue: 0.0690 time to fit residues: 8.6639 Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 127 ASN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 180 LEU 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 42 ASP 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 11 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120218 restraints weight = 5492.012| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.42 r_work: 0.3198 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1829 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 : 0.575 7.985 6121 Z= 0.292 Chirality : 0.043 0.141 692 Planarity : 0.004 0.040 765 Dihedral : 4.463 22.583 595 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.53 % Allowed : 15.77 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.38), residues: 546 helix: 1.61 (0.38), residues: 206 sheet: -0.94 (0.46), residues: 141 loop : -1.44 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.013 0.001 TYR P 134 PHE 0.018 0.001 PHE A 69 TRP 0.011 0.001 TRP P 182 HIS 0.001 0.001 HIS P 211 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4485) covalent geometry : angle 0.57546 ( 6117) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.19942 ( 4) hydrogen bonds : bond 0.02886 ( 225) hydrogen bonds : angle 4.41231 ( 639) *********************** 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 102 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.154 Fit side-chains REVERT: P 207 PHE cc_start: 0.7397 (t80) cc_final: 0.7165 (t80) REVERT: P 356 LEU cc_start: 0.8674 (mp) cc_final: 0.8365 (mp) REVERT: A 55 GLU cc_start: 0.7434 (mp0) cc_final: 0.7166 (mp0) outliers start: 17 outliers final: 17 residues processed: 95 average time/residue: 0.0644 time to fit residues: 8.0002 Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 127 ASN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 180 LEU 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 42 ASP 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 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 17 optimal weight: 0.0770 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.155379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120181 restraints weight = 5455.286| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.41 r_work: 0.3204 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4487 Z= 0.140 Angle : 0.580 8.084 6121 Z= 0.293 Chirality : 0.043 0.144 692 Planarity : 0.004 0.040 765 Dihedral : 4.434 22.629 595 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.53 % Allowed : 16.18 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.38), residues: 546 helix: 1.81 (0.38), residues: 200 sheet: -0.98 (0.46), residues: 142 loop : -1.38 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 24 TYR 0.014 0.001 TYR P 185 PHE 0.017 0.001 PHE A 69 TRP 0.011 0.001 TRP P 182 HIS 0.001 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4485) covalent geometry : angle 0.58008 ( 6117) SS BOND : bond 0.00227 ( 2) SS BOND : angle 0.16253 ( 4) hydrogen bonds : bond 0.02905 ( 225) hydrogen bonds : angle 4.38001 ( 639) ********************** 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 102 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.162 Fit side-chains REVERT: P 207 PHE cc_start: 0.7397 (t80) cc_final: 0.7169 (t80) REVERT: P 356 LEU cc_start: 0.8663 (mp) cc_final: 0.8348 (mp) REVERT: A 55 GLU cc_start: 0.7398 (mp0) cc_final: 0.7130 (mp0) outliers start: 17 outliers final: 16 residues processed: 95 average time/residue: 0.0630 time to fit residues: 7.8150 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 : 0.136 ------------------------------------------------------------------------------- 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 127 ASN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 180 LEU 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 37 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.154467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119019 restraints weight = 5514.744| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.43 r_work: 0.3187 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4487 Z= 0.157 Angle : 0.591 8.048 6121 Z= 0.299 Chirality : 0.044 0.145 692 Planarity : 0.004 0.039 765 Dihedral : 4.467 22.809 595 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.53 % Allowed : 15.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.38), residues: 546 helix: 1.78 (0.37), residues: 200 sheet: -0.98 (0.46), residues: 142 loop : -1.38 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 24 TYR 0.014 0.001 TYR P 134 PHE 0.019 0.001 PHE P 289 TRP 0.013 0.001 TRP P 182 HIS 0.001 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4485) covalent geometry : angle 0.59114 ( 6117) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.20206 ( 4) hydrogen bonds : bond 0.02987 ( 225) hydrogen bonds : angle 4.39601 ( 639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1236.05 seconds wall clock time: 22 minutes 0.11 seconds (1320.11 seconds total)