Starting phenix.real_space_refine on Wed Jul 23 21:22:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dki_27489/07_2025/8dki_27489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dki_27489/07_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_27489/07_2025/8dki_27489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dki_27489/07_2025/8dki_27489.map" model { file = "/net/cci-nas-00/data/ceres_data/8dki_27489/07_2025/8dki_27489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dki_27489/07_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 3.31, 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: 0.98 Conformation dependent library (CDL) restraints added in 536.8 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: 0.52 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: 1.16 Time building geometry restraints manager: 1.18 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: 1.510 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.730 Find NCS groups from input model: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.390 ------------------------------------------------------------------------------- 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 : 0.497 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: 0.1691 time to fit residues: 21.6788 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 : 0.509 ------------------------------------------------------------------------------- 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 = 0.118287 restraints weight = 5206.275| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.04 r_work: 0.3168 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- 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 : 0.443 Fit side-chains REVERT: P 140 ILE cc_start: 0.8735 (tt) cc_final: 0.8519 (tt) REVERT: P 356 LEU cc_start: 0.8635 (mp) cc_final: 0.8344 (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: 0.1575 time to fit residues: 19.2224 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 : 0.449 ------------------------------------------------------------------------------- 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: 0.2980 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: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.153487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119041 restraints weight = 5368.809| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.33 r_work: 0.3194 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1390 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= 0.152 Angle : 0.594 7.751 6121 Z= 0.303 Chirality : 0.043 0.145 692 Planarity : 0.004 0.044 765 Dihedral : 4.615 22.970 595 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: -0.28 (0.38), residues: 546 helix: 1.77 (0.38), residues: 200 sheet: -1.12 (0.43), residues: 151 loop : -1.41 (0.45), residues: 195 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 0.03201 ( 225) hydrogen bonds : angle 4.70576 ( 639) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.25684 ( 4) covalent geometry : bond 0.00356 ( 4485) covalent geometry : angle 0.59462 ( 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 : 0.510 Fit side-chains REVERT: P 140 ILE cc_start: 0.8643 (tt) cc_final: 0.8425 (tt) REVERT: P 341 PHE cc_start: 0.8286 (t80) cc_final: 0.8077 (t80) REVERT: P 356 LEU cc_start: 0.8632 (mp) cc_final: 0.8332 (mp) REVERT: A 31 ASN cc_start: 0.8854 (m-40) cc_final: 0.8554 (m-40) REVERT: A 55 GLU cc_start: 0.7657 (mp0) cc_final: 0.7404 (mp0) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1498 time to fit residues: 19.8338 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 : 0.427 ------------------------------------------------------------------------------- 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: 0.2980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.155425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120571 restraints weight = 5419.439| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.38 r_work: 0.3209 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4487 Z= 0.132 Angle : 0.573 6.862 6121 Z= 0.293 Chirality : 0.043 0.142 692 Planarity : 0.004 0.043 765 Dihedral : 4.467 22.534 595 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.49 % Allowed : 14.11 % Favored : 83.40 % 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: -0.15 (0.38), residues: 546 helix: 1.83 (0.38), residues: 200 sheet: -0.89 (0.46), residues: 141 loop : -1.44 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 PHE 0.014 0.001 PHE A 69 TYR 0.015 0.001 TYR P 134 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 225) hydrogen bonds : angle 4.56237 ( 639) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.17922 ( 4) covalent geometry : bond 0.00305 ( 4485) covalent geometry : angle 0.57314 ( 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 102 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.487 Fit side-chains REVERT: P 356 LEU cc_start: 0.8612 (mp) cc_final: 0.8305 (mp) REVERT: A 55 GLU cc_start: 0.7505 (mp0) cc_final: 0.7243 (mp0) outliers start: 12 outliers final: 11 residues processed: 97 average time/residue: 0.1471 time to fit residues: 18.3972 Evaluate side-chains 95 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 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: 2.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3758 r_free = 0.3758 target = 0.153127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118384 restraints weight = 5493.003| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.36 r_work: 0.3181 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1734 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= 0.170 Angle : 0.591 6.949 6121 Z= 0.301 Chirality : 0.044 0.146 692 Planarity : 0.004 0.042 765 Dihedral : 4.561 22.906 595 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % 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 (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: 1.81 (0.38), residues: 200 sheet: -0.90 (0.46), residues: 142 loop : -1.46 (0.43), residues: 204 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 0.017 0.001 PHE P 207 TYR 0.016 0.002 TYR P 185 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 225) hydrogen bonds : angle 4.55619 ( 639) SS BOND : bond 0.00181 ( 2) SS BOND : angle 0.26290 ( 4) covalent geometry : bond 0.00405 ( 4485) covalent geometry : angle 0.59137 ( 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 96 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.424 Fit side-chains REVERT: P 185 TYR cc_start: 0.7922 (t80) cc_final: 0.7616 (t80) REVERT: P 356 LEU cc_start: 0.8650 (mp) cc_final: 0.8369 (mp) REVERT: A 55 GLU cc_start: 0.7539 (mp0) cc_final: 0.7271 (mp0) REVERT: B 61 ARG cc_start: 0.8381 (ttm170) cc_final: 0.7995 (ttm170) outliers start: 13 outliers final: 13 residues processed: 91 average time/residue: 0.1477 time to fit residues: 17.4436 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 : 0.482 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120919 restraints weight = 5401.192| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.37 r_work: 0.3218 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4487 Z= 0.130 Angle : 0.566 7.149 6121 Z= 0.288 Chirality : 0.043 0.141 692 Planarity : 0.004 0.041 765 Dihedral : 4.442 22.407 595 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.11 % Allowed : 16.60 % 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 (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: -0.11 (0.38), residues: 546 helix: 1.85 (0.38), residues: 200 sheet: -0.85 (0.47), residues: 141 loop : -1.42 (0.43), 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 105 PHE 0.014 0.001 PHE P 341 TYR 0.014 0.001 TYR P 134 ARG 0.005 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 225) hydrogen bonds : angle 4.46436 ( 639) SS BOND : bond 0.00232 ( 2) SS BOND : angle 0.17286 ( 4) covalent geometry : bond 0.00304 ( 4485) covalent geometry : angle 0.56631 ( 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 106 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.488 Fit side-chains REVERT: P 356 LEU cc_start: 0.8632 (mp) cc_final: 0.8344 (mp) REVERT: A 55 GLU cc_start: 0.7382 (mp0) cc_final: 0.7106 (mp0) outliers start: 15 outliers final: 14 residues processed: 100 average time/residue: 0.1479 time to fit residues: 19.1611 Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 189 GLN A 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115476 restraints weight = 5487.349| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.35 r_work: 0.3152 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4487 Z= 0.249 Angle : 0.652 7.406 6121 Z= 0.332 Chirality : 0.047 0.151 692 Planarity : 0.004 0.040 765 Dihedral : 4.816 23.635 595 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.73 % Allowed : 16.39 % 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: -0.45 (0.37), residues: 546 helix: 1.50 (0.37), residues: 206 sheet: -0.97 (0.47), residues: 142 loop : -1.67 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 182 HIS 0.002 0.001 HIS B 55 PHE 0.022 0.002 PHE A 69 TYR 0.018 0.002 TYR P 134 ARG 0.007 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 225) hydrogen bonds : angle 4.69504 ( 639) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.49389 ( 4) covalent geometry : bond 0.00601 ( 4485) covalent geometry : angle 0.65166 ( 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 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.456 Fit side-chains REVERT: P 148 MET cc_start: 0.8364 (ttp) cc_final: 0.7754 (ttp) REVERT: P 356 LEU cc_start: 0.8739 (mp) cc_final: 0.8397 (mp) REVERT: A 55 GLU cc_start: 0.7694 (mp0) cc_final: 0.7392 (mp0) REVERT: B 61 ARG cc_start: 0.8390 (ttm170) cc_final: 0.7954 (ttm170) outliers start: 18 outliers final: 16 residues processed: 95 average time/residue: 0.1395 time to fit residues: 17.3265 Evaluate side-chains 96 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.155015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120362 restraints weight = 5430.774| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.36 r_work: 0.3207 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4487 Z= 0.132 Angle : 0.582 7.805 6121 Z= 0.296 Chirality : 0.043 0.144 692 Planarity : 0.004 0.039 765 Dihedral : 4.513 22.496 595 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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: -0.27 (0.38), residues: 546 helix: 1.60 (0.37), residues: 206 sheet: -0.89 (0.46), residues: 141 loop : -1.49 (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 102 PHE 0.017 0.001 PHE P 207 TYR 0.016 0.001 TYR P 185 ARG 0.006 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 225) hydrogen bonds : angle 4.50690 ( 639) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.16266 ( 4) covalent geometry : bond 0.00306 ( 4485) covalent geometry : angle 0.58169 ( 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 112 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.440 Fit side-chains REVERT: P 148 MET cc_start: 0.8191 (ttp) cc_final: 0.7665 (ttp) REVERT: P 356 LEU cc_start: 0.8671 (mp) cc_final: 0.8353 (mp) REVERT: A 55 GLU cc_start: 0.7386 (mp0) cc_final: 0.7116 (mp0) outliers start: 15 outliers final: 14 residues processed: 106 average time/residue: 0.1483 time to fit residues: 20.4329 Evaluate side-chains 109 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 0.0010 overall best weight: 0.4524 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.156037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123228 restraints weight = 5166.752| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.05 r_work: 0.3219 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1986 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= 0.126 Angle : 0.578 8.025 6121 Z= 0.294 Chirality : 0.043 0.141 692 Planarity : 0.004 0.039 765 Dihedral : 4.419 22.177 595 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.90 % Allowed : 17.22 % 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: -0.09 (0.38), residues: 546 helix: 1.90 (0.38), residues: 200 sheet: -0.91 (0.48), residues: 136 loop : -1.38 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 182 HIS 0.001 0.001 HIS P 211 PHE 0.025 0.001 PHE P 207 TYR 0.015 0.001 TYR P 185 ARG 0.007 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 225) hydrogen bonds : angle 4.37071 ( 639) SS BOND : bond 0.00226 ( 2) SS BOND : angle 0.15370 ( 4) covalent geometry : bond 0.00291 ( 4485) covalent geometry : angle 0.57825 ( 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: 14 poor density : 93 time to evaluate : 0.466 Fit side-chains REVERT: P 356 LEU cc_start: 0.8669 (mp) cc_final: 0.8349 (mp) REVERT: A 55 GLU cc_start: 0.7571 (mp0) cc_final: 0.7260 (mp0) REVERT: B 61 ARG cc_start: 0.8375 (ttm170) cc_final: 0.7937 (ttm170) outliers start: 14 outliers final: 13 residues processed: 100 average time/residue: 0.2105 time to fit residues: 26.9731 Evaluate side-chains 104 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 45 optimal weight: 0.0170 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 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: 0.4980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.156011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122896 restraints weight = 5095.648| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.05 r_work: 0.3215 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2067 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= 0.136 Angle : 0.586 8.113 6121 Z= 0.298 Chirality : 0.043 0.142 692 Planarity : 0.004 0.039 765 Dihedral : 4.427 22.283 595 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.70 % Allowed : 18.05 % 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: 1.92 (0.38), residues: 200 sheet: -0.90 (0.47), residues: 141 loop : -1.37 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 182 HIS 0.001 0.001 HIS P 211 PHE 0.022 0.001 PHE P 207 TYR 0.014 0.002 TYR P 185 ARG 0.008 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 225) hydrogen bonds : angle 4.32060 ( 639) SS BOND : bond 0.00224 ( 2) SS BOND : angle 0.16302 ( 4) covalent geometry : bond 0.00319 ( 4485) covalent geometry : angle 0.58667 ( 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 110 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.441 Fit side-chains REVERT: P 140 ILE cc_start: 0.8601 (tt) cc_final: 0.8333 (pt) REVERT: P 174 SER cc_start: 0.8574 (p) cc_final: 0.8325 (p) REVERT: P 356 LEU cc_start: 0.8667 (mp) cc_final: 0.8343 (mp) REVERT: A 55 GLU cc_start: 0.7556 (mp0) cc_final: 0.7239 (mp0) outliers start: 13 outliers final: 13 residues processed: 104 average time/residue: 0.1468 time to fit residues: 19.7195 Evaluate side-chains 106 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 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 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.0070 chunk 23 optimal weight: 1.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.158786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125796 restraints weight = 5112.125| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.06 r_work: 0.3243 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4487 Z= 0.119 Angle : 0.574 8.168 6121 Z= 0.292 Chirality : 0.043 0.140 692 Planarity : 0.004 0.039 765 Dihedral : 4.308 21.786 595 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.70 % Allowed : 18.88 % 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: 0.03 (0.39), residues: 546 helix: 2.01 (0.38), residues: 200 sheet: -0.83 (0.47), residues: 141 loop : -1.33 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 182 HIS 0.001 0.000 HIS P 211 PHE 0.025 0.001 PHE P 207 TYR 0.015 0.001 TYR P 185 ARG 0.008 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 225) hydrogen bonds : angle 4.25574 ( 639) SS BOND : bond 0.00236 ( 2) SS BOND : angle 0.11687 ( 4) covalent geometry : bond 0.00274 ( 4485) covalent geometry : angle 0.57416 ( 6117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2734.55 seconds wall clock time: 48 minutes 38.18 seconds (2918.18 seconds total)