Starting phenix.real_space_refine on Tue Feb 3 14:33:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mqr_48537/02_2026/9mqr_48537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mqr_48537/02_2026/9mqr_48537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mqr_48537/02_2026/9mqr_48537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mqr_48537/02_2026/9mqr_48537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mqr_48537/02_2026/9mqr_48537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mqr_48537/02_2026/9mqr_48537.map" } resolution = 3.16 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= 0.000 sd= 0.027 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 19 5.16 5 C 2354 2.51 5 N 635 2.21 5 O 721 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3729 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1875 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 11, 'TRANS': 233} Chain breaks: 4 Chain: "D" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1046 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 1.06, per 1000 atoms: 0.28 Number of scatterers: 3729 At special positions: 0 Unit cell: (63.525, 80.85, 105.6, 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 19 16.00 O 721 8.00 N 635 7.00 C 2354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 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: 0.31 Conformation dependent library (CDL) restraints added in 148.4 milliseconds 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 900 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 17.8% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 293 through 311 removed outlier: 3.595A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.552A pdb=" N GLU A 316 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 343 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.861A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.233A pdb=" N GLU D 107 " --> pdb=" O TYR D 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 353 removed outlier: 5.080A pdb=" N SER A 532 " --> pdb=" O TRP A 498 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 348 through 353 removed outlier: 3.708A pdb=" N HIS A 539 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 513 through 518 removed outlier: 6.788A pdb=" N THR A 524 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER A 518 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY A 375 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLY E 64 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AA5, first strand: chain 'D' and resid 14 through 15 removed outlier: 6.750A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL D 51 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR D 63 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER D 53 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR D 61 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 101 through 103 removed outlier: 6.813A pdb=" N ARG D 101 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.506A pdb=" N VAL E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR E 49 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 13 187 hydrogen bonds defined for protein. 465 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: 0.62 Time building geometry restraints manager: 0.43 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: 1057 1.33 - 1.45: 648 1.45 - 1.57: 2075 1.57 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 3809 Sorted by residual: bond pdb=" N ASP D 121 " pdb=" CA ASP D 121 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.28e-02 6.10e+03 5.07e+00 bond pdb=" N ASN D 87 " pdb=" CA ASN D 87 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.41e-02 5.03e+03 4.82e+00 bond pdb=" C SER D 10 " pdb=" O SER D 10 " ideal model delta sigma weight residual 1.235 1.213 0.022 1.00e-02 1.00e+04 4.78e+00 bond pdb=" CA SER D 10 " pdb=" CB SER D 10 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.93e-02 2.68e+03 3.91e+00 bond pdb=" N GLU D 9 " pdb=" CA GLU D 9 " ideal model delta sigma weight residual 1.452 1.477 -0.024 1.25e-02 6.40e+03 3.80e+00 ... (remaining 3804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 5019 1.42 - 2.85: 110 2.85 - 4.27: 30 4.27 - 5.70: 3 5.70 - 7.12: 5 Bond angle restraints: 5167 Sorted by residual: angle pdb=" CA ASP D 121 " pdb=" CB ASP D 121 " pdb=" CG ASP D 121 " ideal model delta sigma weight residual 112.60 119.72 -7.12 1.00e+00 1.00e+00 5.07e+01 angle pdb=" C GLN E 27 " pdb=" CA GLN E 27 " pdb=" CB GLN E 27 " ideal model delta sigma weight residual 116.54 111.29 5.25 1.15e+00 7.56e-01 2.09e+01 angle pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" O LEU D 120 " ideal model delta sigma weight residual 120.92 117.24 3.68 1.04e+00 9.25e-01 1.25e+01 angle pdb=" CA GLU D 9 " pdb=" C GLU D 9 " pdb=" O GLU D 9 " ideal model delta sigma weight residual 121.82 117.69 4.13 1.21e+00 6.83e-01 1.16e+01 angle pdb=" C ASP D 121 " pdb=" CA ASP D 121 " pdb=" CB ASP D 121 " ideal model delta sigma weight residual 110.11 116.44 -6.33 1.89e+00 2.80e-01 1.12e+01 ... (remaining 5162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 1915 16.14 - 32.28: 256 32.28 - 48.42: 78 48.42 - 64.57: 22 64.57 - 80.71: 4 Dihedral angle restraints: 2275 sinusoidal: 877 harmonic: 1398 Sorted by residual: dihedral pdb=" CB CYS A 513 " pdb=" SG CYS A 513 " pdb=" SG CYS A 527 " pdb=" CB CYS A 527 " ideal model delta sinusoidal sigma weight residual 93.00 131.39 -38.39 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" C ASP D 121 " pdb=" N ASP D 121 " pdb=" CA ASP D 121 " pdb=" CB ASP D 121 " ideal model delta harmonic sigma weight residual -122.60 -131.43 8.83 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" CA ASP E 70 " pdb=" CB ASP E 70 " pdb=" CG ASP E 70 " pdb=" OD1 ASP E 70 " ideal model delta sinusoidal sigma weight residual -30.00 -89.74 59.74 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 2272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 460 0.052 - 0.104: 95 0.104 - 0.156: 23 0.156 - 0.208: 1 0.208 - 0.260: 2 Chirality restraints: 581 Sorted by residual: chirality pdb=" CA MET D 86 " pdb=" N MET D 86 " pdb=" C MET D 86 " pdb=" CB MET D 86 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASP D 121 " pdb=" N ASP D 121 " pdb=" C ASP D 121 " pdb=" CB ASP D 121 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA LEU D 120 " pdb=" N LEU D 120 " pdb=" C LEU D 120 " pdb=" CB LEU D 120 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 578 not shown) Planarity restraints: 656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 8 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C VAL D 8 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL D 8 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D 9 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 267 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 268 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 7 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO E 8 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 8 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 8 " 0.018 5.00e-02 4.00e+02 ... (remaining 653 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1000 2.80 - 3.33: 3130 3.33 - 3.85: 5972 3.85 - 4.38: 7019 4.38 - 4.90: 12917 Nonbonded interactions: 30038 Sorted by model distance: nonbonded pdb=" O PRO E 8 " pdb=" OG SER E 9 " model vdw 2.276 3.040 nonbonded pdb=" NZ LYS E 39 " pdb=" O GLU E 81 " model vdw 2.289 3.120 nonbonded pdb=" OH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 2.343 3.040 nonbonded pdb=" OD2 ASP A 306 " pdb=" OG SER A 354 " model vdw 2.378 3.040 nonbonded pdb=" O VAL A 387 " pdb=" NE2 HIS A 452 " model vdw 2.378 3.120 ... (remaining 30033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.000 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.004 0.042 3813 Z= 0.198 Angle : 0.587 7.123 5175 Z= 0.344 Chirality : 0.046 0.260 581 Planarity : 0.005 0.045 656 Dihedral : 16.650 80.707 1363 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 25.55 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.56 (0.40), residues: 470 helix: 1.59 (0.62), residues: 66 sheet: -0.59 (0.41), residues: 182 loop : -0.68 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 66 TYR 0.009 0.001 TYR D 98 PHE 0.006 0.001 PHE A 278 TRP 0.010 0.001 TRP D 50 HIS 0.002 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 3809) covalent geometry : angle 0.58755 ( 5167) SS BOND : bond 0.00227 ( 4) SS BOND : angle 0.36551 ( 8) hydrogen bonds : bond 0.19800 ( 162) hydrogen bonds : angle 8.92382 ( 465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 440 ARG cc_start: 0.7340 (mtp85) cc_final: 0.6752 (ttt180) REVERT: D 104 TYR cc_start: 0.8180 (m-80) cc_final: 0.7854 (m-80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0767 time to fit residues: 4.9358 Evaluate side-chains 49 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.104907 restraints weight = 4807.503| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.61 r_work: 0.3035 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3813 Z= 0.131 Angle : 0.522 5.939 5175 Z= 0.280 Chirality : 0.043 0.138 581 Planarity : 0.005 0.043 656 Dihedral : 4.415 19.129 517 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.22 % Allowed : 25.79 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.56 (0.40), residues: 470 helix: 1.49 (0.60), residues: 67 sheet: -0.71 (0.39), residues: 200 loop : -0.48 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 66 TYR 0.008 0.001 TYR D 35 PHE 0.009 0.001 PHE A 466 TRP 0.010 0.001 TRP D 50 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3809) covalent geometry : angle 0.52198 ( 5167) SS BOND : bond 0.00270 ( 4) SS BOND : angle 0.53689 ( 8) hydrogen bonds : bond 0.04117 ( 162) hydrogen bonds : angle 5.58677 ( 465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.094 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.0596 time to fit residues: 3.9560 Evaluate side-chains 45 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain D residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.103955 restraints weight = 4803.474| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.57 r_work: 0.3043 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3813 Z= 0.164 Angle : 0.537 5.992 5175 Z= 0.285 Chirality : 0.044 0.139 581 Planarity : 0.005 0.044 656 Dihedral : 4.500 19.805 517 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.16 % Allowed : 25.79 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.71 (0.39), residues: 470 helix: 0.85 (0.59), residues: 73 sheet: -0.71 (0.40), residues: 187 loop : -0.55 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 66 TYR 0.016 0.001 TYR D 35 PHE 0.008 0.001 PHE A 466 TRP 0.008 0.001 TRP D 50 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3809) covalent geometry : angle 0.53695 ( 5167) SS BOND : bond 0.00411 ( 4) SS BOND : angle 0.80258 ( 8) hydrogen bonds : bond 0.03902 ( 162) hydrogen bonds : angle 5.20622 ( 465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.088 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.0523 time to fit residues: 3.6287 Evaluate side-chains 53 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100728 restraints weight = 4809.454| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.59 r_work: 0.2980 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 3813 Z= 0.283 Angle : 0.626 6.292 5175 Z= 0.330 Chirality : 0.048 0.156 581 Planarity : 0.005 0.053 656 Dihedral : 4.900 20.694 517 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.87 % Allowed : 26.28 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.99 (0.38), residues: 470 helix: 0.52 (0.57), residues: 73 sheet: -0.65 (0.40), residues: 186 loop : -0.95 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 66 TYR 0.015 0.002 TYR D 35 PHE 0.011 0.002 PHE A 497 TRP 0.010 0.002 TRP D 50 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00684 ( 3809) covalent geometry : angle 0.62507 ( 5167) SS BOND : bond 0.00429 ( 4) SS BOND : angle 0.87839 ( 8) hydrogen bonds : bond 0.04387 ( 162) hydrogen bonds : angle 5.32799 ( 465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.088 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 60 average time/residue: 0.0463 time to fit residues: 3.5056 Evaluate side-chains 56 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102675 restraints weight = 4818.167| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.63 r_work: 0.3017 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3813 Z= 0.151 Angle : 0.527 5.976 5175 Z= 0.282 Chirality : 0.044 0.174 581 Planarity : 0.005 0.050 656 Dihedral : 4.646 20.161 517 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.16 % Allowed : 27.25 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.85 (0.39), residues: 470 helix: 0.67 (0.59), residues: 73 sheet: -0.58 (0.40), residues: 185 loop : -0.87 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 66 TYR 0.014 0.001 TYR D 35 PHE 0.008 0.001 PHE A 464 TRP 0.009 0.001 TRP D 50 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3809) covalent geometry : angle 0.52694 ( 5167) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.53057 ( 8) hydrogen bonds : bond 0.03599 ( 162) hydrogen bonds : angle 5.03670 ( 465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.142 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 53 average time/residue: 0.0713 time to fit residues: 4.6970 Evaluate side-chains 52 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101867 restraints weight = 4877.999| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.60 r_work: 0.3009 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3813 Z= 0.180 Angle : 0.545 6.015 5175 Z= 0.289 Chirality : 0.045 0.158 581 Planarity : 0.005 0.051 656 Dihedral : 4.656 20.250 517 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.89 % Allowed : 26.28 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.90 (0.39), residues: 470 helix: 0.65 (0.58), residues: 73 sheet: -0.59 (0.40), residues: 185 loop : -0.92 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 66 TYR 0.018 0.001 TYR D 35 PHE 0.007 0.001 PHE A 466 TRP 0.008 0.001 TRP D 50 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 3809) covalent geometry : angle 0.54516 ( 5167) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.57215 ( 8) hydrogen bonds : bond 0.03684 ( 162) hydrogen bonds : angle 5.00465 ( 465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.147 Fit side-chains outliers start: 16 outliers final: 16 residues processed: 56 average time/residue: 0.0672 time to fit residues: 4.6984 Evaluate side-chains 58 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.103090 restraints weight = 4865.789| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.57 r_work: 0.3030 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3813 Z= 0.165 Angle : 0.536 6.007 5175 Z= 0.285 Chirality : 0.044 0.149 581 Planarity : 0.005 0.052 656 Dihedral : 4.626 20.164 517 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.87 % Allowed : 25.06 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.87 (0.39), residues: 470 helix: 0.66 (0.58), residues: 73 sheet: -0.58 (0.40), residues: 185 loop : -0.89 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 66 TYR 0.019 0.001 TYR D 35 PHE 0.007 0.001 PHE A 466 TRP 0.008 0.001 TRP D 50 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3809) covalent geometry : angle 0.53559 ( 5167) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.51536 ( 8) hydrogen bonds : bond 0.03566 ( 162) hydrogen bonds : angle 4.93160 ( 465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.090 Fit side-chains outliers start: 20 outliers final: 18 residues processed: 60 average time/residue: 0.0493 time to fit residues: 3.7226 Evaluate side-chains 60 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.103248 restraints weight = 4860.188| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.55 r_work: 0.3023 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3813 Z= 0.167 Angle : 0.556 6.942 5175 Z= 0.290 Chirality : 0.044 0.144 581 Planarity : 0.005 0.051 656 Dihedral : 4.599 20.113 517 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.35 % Allowed : 24.57 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.86 (0.39), residues: 470 helix: 0.68 (0.58), residues: 73 sheet: -0.57 (0.39), residues: 184 loop : -0.89 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 90 TYR 0.020 0.001 TYR D 35 PHE 0.007 0.001 PHE A 466 TRP 0.009 0.001 TRP D 50 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3809) covalent geometry : angle 0.55573 ( 5167) SS BOND : bond 0.00310 ( 4) SS BOND : angle 0.48764 ( 8) hydrogen bonds : bond 0.03538 ( 162) hydrogen bonds : angle 4.92589 ( 465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.143 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 61 average time/residue: 0.0797 time to fit residues: 6.0556 Evaluate side-chains 61 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 HIS ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.103072 restraints weight = 4804.114| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.64 r_work: 0.3012 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3813 Z= 0.170 Angle : 0.558 6.392 5175 Z= 0.292 Chirality : 0.044 0.142 581 Planarity : 0.005 0.051 656 Dihedral : 4.607 20.113 517 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.62 % Allowed : 24.82 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.87 (0.39), residues: 470 helix: 0.67 (0.58), residues: 73 sheet: -0.59 (0.39), residues: 185 loop : -0.88 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 66 TYR 0.020 0.001 TYR D 35 PHE 0.008 0.001 PHE A 466 TRP 0.009 0.001 TRP D 50 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3809) covalent geometry : angle 0.55811 ( 5167) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.46940 ( 8) hydrogen bonds : bond 0.03545 ( 162) hydrogen bonds : angle 4.92236 ( 465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.146 Fit side-chains outliers start: 19 outliers final: 19 residues processed: 58 average time/residue: 0.0772 time to fit residues: 5.5897 Evaluate side-chains 61 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 41 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.104404 restraints weight = 4807.178| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.57 r_work: 0.3042 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3813 Z= 0.144 Angle : 0.539 6.429 5175 Z= 0.283 Chirality : 0.044 0.139 581 Planarity : 0.005 0.050 656 Dihedral : 4.527 20.033 517 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.62 % Allowed : 24.57 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.78 (0.39), residues: 470 helix: 0.75 (0.58), residues: 73 sheet: -0.52 (0.40), residues: 184 loop : -0.84 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 90 TYR 0.019 0.001 TYR D 35 PHE 0.008 0.001 PHE A 466 TRP 0.009 0.001 TRP D 50 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3809) covalent geometry : angle 0.53962 ( 5167) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.43880 ( 8) hydrogen bonds : bond 0.03395 ( 162) hydrogen bonds : angle 4.83590 ( 465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.162 Fit side-chains REVERT: A 259 MET cc_start: 0.6770 (mmt) cc_final: 0.6421 (mmm) outliers start: 19 outliers final: 17 residues processed: 57 average time/residue: 0.0713 time to fit residues: 5.1814 Evaluate side-chains 58 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103505 restraints weight = 4744.364| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.61 r_work: 0.3029 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3813 Z= 0.166 Angle : 0.553 6.014 5175 Z= 0.290 Chirality : 0.044 0.140 581 Planarity : 0.005 0.050 656 Dihedral : 4.574 20.164 517 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.62 % Allowed : 24.57 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -0.80 (0.39), residues: 470 helix: 0.71 (0.58), residues: 73 sheet: -0.52 (0.40), residues: 184 loop : -0.86 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 90 TYR 0.019 0.001 TYR D 35 PHE 0.009 0.001 PHE A 466 TRP 0.009 0.001 TRP D 50 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 3809) covalent geometry : angle 0.55264 ( 5167) SS BOND : bond 0.00307 ( 4) SS BOND : angle 0.45638 ( 8) hydrogen bonds : bond 0.03505 ( 162) hydrogen bonds : angle 4.88059 ( 465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1120.33 seconds wall clock time: 19 minutes 55.89 seconds (1195.89 seconds total)