Starting phenix.real_space_refine on Tue Aug 4 16:04:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rh5_53958/08_2026/9rh5_53958.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rh5_53958/08_2026/9rh5_53958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rh5_53958/08_2026/9rh5_53958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rh5_53958/08_2026/9rh5_53958.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rh5_53958/08_2026/9rh5_53958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rh5_53958/08_2026/9rh5_53958.map" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3013 2.51 5 N 755 2.21 5 O 836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4623 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2900 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 15, 'TRANS': 370} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Time building chain proxies: 1.21, per 1000 atoms: 0.26 Number of scatterers: 4623 At special positions: 0 Unit cell: (68.634, 76.167, 102.951, 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 836 8.00 N 755 7.00 C 3013 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 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: 0.40 Conformation dependent library (CDL) restraints added in 185.3 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 53.6% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.681A pdb=" N GLY A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TRP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 85 removed outlier: 3.559A pdb=" N MET A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 117 removed outlier: 4.902A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix Proline residue: A 108 - end of helix removed outlier: 3.891A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.566A pdb=" N GLU A 124 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 126 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.612A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 149 through 175 Processing helix chain 'A' and resid 180 through 200 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.647A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.896A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 384 removed outlier: 3.586A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.516A pdb=" N ASP B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'C' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.514A pdb=" N LYS B 3 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.093A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU B 45 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.639A pdb=" N CYS B 96 " --> pdb=" O TRP B 108 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRP B 108 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS B 98 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.524A pdb=" N ILE C 75 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.687A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.703A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 834 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: 0.76 Time building geometry restraints manager: 0.53 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: 975 1.33 - 1.45: 1053 1.45 - 1.57: 2668 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4727 Sorted by residual: bond pdb=" C THR C 7 " pdb=" N PRO C 8 " ideal model delta sigma weight residual 1.335 1.365 -0.030 8.70e-03 1.32e+04 1.18e+01 bond pdb=" C ARG A 6 " pdb=" O ARG A 6 " ideal model delta sigma weight residual 1.236 1.277 -0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" N ARG A 6 " pdb=" CA ARG A 6 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.33e-02 5.65e+03 7.87e+00 bond pdb=" N ASP A 11 " pdb=" CA ASP A 11 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.60e+00 bond pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.41e-02 5.03e+03 6.33e+00 ... (remaining 4722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 6230 1.97 - 3.93: 154 3.93 - 5.90: 35 5.90 - 7.86: 9 7.86 - 9.83: 2 Bond angle restraints: 6430 Sorted by residual: angle pdb=" C ASP A 11 " pdb=" CA ASP A 11 " pdb=" CB ASP A 11 " ideal model delta sigma weight residual 110.42 118.25 -7.83 1.99e+00 2.53e-01 1.55e+01 angle pdb=" CA ASP B 90 " pdb=" CB ASP B 90 " pdb=" CG ASP B 90 " ideal model delta sigma weight residual 112.60 116.48 -3.88 1.00e+00 1.00e+00 1.50e+01 angle pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " ideal model delta sigma weight residual 112.60 119.13 -6.53 1.70e+00 3.46e-01 1.48e+01 angle pdb=" N ILE C 29 " pdb=" CA ILE C 29 " pdb=" C ILE C 29 " ideal model delta sigma weight residual 113.53 109.97 3.56 9.80e-01 1.04e+00 1.32e+01 angle pdb=" N SER B 88 " pdb=" CA SER B 88 " pdb=" C SER B 88 " ideal model delta sigma weight residual 113.19 109.14 4.05 1.19e+00 7.06e-01 1.16e+01 ... (remaining 6425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 2483 15.97 - 31.94: 216 31.94 - 47.91: 45 47.91 - 63.88: 18 63.88 - 79.84: 3 Dihedral angle restraints: 2765 sinusoidal: 1027 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.47 40.53 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CA GLU B 99 " pdb=" C GLU B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASN B 103 " pdb=" C ASN B 103 " pdb=" N ASP B 104 " pdb=" CA ASP B 104 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 2762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 596 0.046 - 0.093: 129 0.093 - 0.139: 28 0.139 - 0.186: 5 0.186 - 0.232: 2 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA ASP A 11 " pdb=" N ASP A 11 " pdb=" C ASP A 11 " pdb=" CB ASP A 11 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CG LEU B 83 " pdb=" CB LEU B 83 " pdb=" CD1 LEU B 83 " pdb=" CD2 LEU B 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU A 143 " pdb=" CB LEU A 143 " pdb=" CD1 LEU A 143 " pdb=" CD2 LEU A 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 757 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 381 " -0.135 9.50e-02 1.11e+02 6.63e-02 1.12e+01 pdb=" NE ARG A 381 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 381 " 0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 381 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 381 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 248 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ALA A 248 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA A 248 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS A 249 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 245 " 0.154 9.50e-02 1.11e+02 6.92e-02 2.95e+00 pdb=" NE ARG A 245 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 245 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 245 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 245 " 0.006 2.00e-02 2.50e+03 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 460 2.75 - 3.28: 4541 3.28 - 3.82: 7679 3.82 - 4.36: 9070 4.36 - 4.90: 15825 Nonbonded interactions: 37575 Sorted by model distance: nonbonded pdb=" O SER C 30 " pdb=" OG SER C 30 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLU B 33 " pdb=" NE2 HIS B 35 " model vdw 2.243 3.120 nonbonded pdb=" NE2 GLN B 39 " pdb=" OE1 GLN C 38 " model vdw 2.277 3.120 nonbonded pdb=" OH TYR A 38 " pdb=" O PHE A 269 " model vdw 2.279 3.040 nonbonded pdb=" O ILE A 27 " pdb=" OG SER A 31 " model vdw 2.323 3.040 ... (remaining 37570 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: 1.280 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 0.048 4729 Z= 0.238 Angle : 0.802 9.828 6434 Z= 0.463 Chirality : 0.043 0.232 760 Planarity : 0.005 0.069 792 Dihedral : 13.333 79.844 1651 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.07 (0.34), residues: 604 helix: 1.27 (0.30), residues: 290 sheet: 1.52 (0.50), residues: 110 loop : -0.51 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.002 ARG A 381 TYR 0.008 0.001 TYR C 49 PHE 0.011 0.001 PHE A 350 TRP 0.025 0.002 TRP C 35 HIS 0.006 0.001 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.24 ( 4727) covalent geometry : angle 0.80165 / 0.46 ( 6430) SS BOND : bond 0.00428 / 0.21 ( 2) SS BOND : angle 1.24218 / 0.69 ( 4) hydrogen bonds : bond 0.20640 / 14.70 ( 285) hydrogen bonds : angle 7.50223 / 5.36 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 242 LYS cc_start: 0.7070 (tttt) cc_final: 0.6682 (ttmt) REVERT: B 34 MET cc_start: 0.6333 (tpt) cc_final: 0.5730 (mtt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0885 time to fit residues: 6.8812 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.0170 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 177 ASN A 256 HIS B 5 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.211850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145909 restraints weight = 5161.855| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.25 r_work: 0.3245 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4729 Z= 0.113 Angle : 0.570 6.700 6434 Z= 0.291 Chirality : 0.040 0.152 760 Planarity : 0.003 0.028 792 Dihedral : 4.187 20.674 650 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.24 % Allowed : 9.80 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.70 (0.34), residues: 604 helix: 1.93 (0.29), residues: 293 sheet: 1.62 (0.50), residues: 106 loop : -0.30 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.013 0.001 TYR C 49 PHE 0.011 0.001 PHE A 8 TRP 0.013 0.001 TRP C 35 HIS 0.002 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 4727) covalent geometry : angle 0.56983 / 0.29 ( 6430) SS BOND : bond 0.00355 / 0.17 ( 2) SS BOND : angle 0.85131 / 0.52 ( 4) hydrogen bonds : bond 0.03971 / 2.77 ( 285) hydrogen bonds : angle 5.29264 / 3.82 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.7192 (tttt) cc_final: 0.6563 (ttmt) REVERT: A 246 SER cc_start: 0.8543 (p) cc_final: 0.8213 (p) REVERT: A 379 TRP cc_start: 0.7268 (OUTLIER) cc_final: 0.6688 (m-10) REVERT: B 60 TYR cc_start: 0.7752 (m-80) cc_final: 0.7238 (m-80) outliers start: 11 outliers final: 5 residues processed: 60 average time/residue: 0.0954 time to fit residues: 7.1138 Evaluate side-chains 52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 381 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN B 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.215382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150512 restraints weight = 5097.250| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.09 r_work: 0.3261 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4729 Z= 0.104 Angle : 0.511 6.609 6434 Z= 0.261 Chirality : 0.038 0.149 760 Planarity : 0.003 0.027 792 Dihedral : 3.961 19.435 650 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.63 % Allowed : 11.22 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.87 (0.34), residues: 604 helix: 2.15 (0.30), residues: 293 sheet: 1.60 (0.50), residues: 106 loop : -0.29 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.012 0.001 TYR C 49 PHE 0.006 0.001 PHE A 72 TRP 0.010 0.001 TRP A 216 HIS 0.001 0.000 HIS B 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 4727) covalent geometry : angle 0.51063 / 0.26 ( 6430) SS BOND : bond 0.00283 / 0.14 ( 2) SS BOND : angle 0.49582 / 0.30 ( 4) hydrogen bonds : bond 0.03452 / 2.40 ( 285) hydrogen bonds : angle 4.95550 / 3.58 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7981 (mt0) cc_final: 0.7714 (pt0) REVERT: A 246 SER cc_start: 0.8605 (p) cc_final: 0.8268 (p) REVERT: A 315 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7357 (mmmt) REVERT: A 379 TRP cc_start: 0.7303 (OUTLIER) cc_final: 0.6744 (m-10) outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.0880 time to fit residues: 6.0867 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.212209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147861 restraints weight = 5121.104| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.44 r_work: 0.3119 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4729 Z= 0.216 Angle : 0.590 6.548 6434 Z= 0.300 Chirality : 0.041 0.147 760 Planarity : 0.004 0.027 792 Dihedral : 4.127 21.351 650 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.65 % Allowed : 11.84 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.76 (0.35), residues: 604 helix: 2.10 (0.30), residues: 291 sheet: 1.63 (0.50), residues: 107 loop : -0.45 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.017 0.002 TYR C 49 PHE 0.015 0.002 PHE A 72 TRP 0.009 0.002 TRP A 379 HIS 0.003 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 ( 4727) covalent geometry : angle 0.59030 / 0.30 ( 6430) SS BOND : bond 0.00290 / 0.14 ( 2) SS BOND : angle 0.54134 / 0.36 ( 4) hydrogen bonds : bond 0.03993 / 2.78 ( 285) hydrogen bonds : angle 4.96094 / 3.59 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7732 (tt0) REVERT: A 242 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6190 (mttt) REVERT: A 379 TRP cc_start: 0.7465 (OUTLIER) cc_final: 0.6779 (m-10) REVERT: C 56 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7894 (m) outliers start: 13 outliers final: 6 residues processed: 61 average time/residue: 0.0913 time to fit residues: 7.0197 Evaluate side-chains 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.0980 chunk 49 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.0470 chunk 46 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 256 HIS B 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.214192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149696 restraints weight = 5105.455| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.12 r_work: 0.3247 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4729 Z= 0.093 Angle : 0.477 6.026 6434 Z= 0.246 Chirality : 0.038 0.145 760 Planarity : 0.003 0.026 792 Dihedral : 3.829 18.575 650 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.06 % Allowed : 12.65 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.96 (0.35), residues: 604 helix: 2.26 (0.30), residues: 291 sheet: 1.84 (0.51), residues: 105 loop : -0.40 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.011 0.001 TYR C 49 PHE 0.006 0.001 PHE A 350 TRP 0.011 0.001 TRP A 62 HIS 0.001 0.000 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 4727) covalent geometry : angle 0.47688 / 0.25 ( 6430) SS BOND : bond 0.00222 / 0.11 ( 2) SS BOND : angle 0.40469 / 0.24 ( 4) hydrogen bonds : bond 0.03099 / 2.15 ( 285) hydrogen bonds : angle 4.65699 / 3.37 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8681 (tpp) cc_final: 0.8178 (tpp) REVERT: A 242 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6030 (mttt) REVERT: A 245 ARG cc_start: 0.8007 (ttt180) cc_final: 0.7650 (ptm160) REVERT: A 246 SER cc_start: 0.8594 (p) cc_final: 0.8220 (p) REVERT: A 379 TRP cc_start: 0.7244 (OUTLIER) cc_final: 0.6453 (m100) outliers start: 15 outliers final: 7 residues processed: 69 average time/residue: 0.0658 time to fit residues: 5.6906 Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.213240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151551 restraints weight = 5237.433| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.30 r_work: 0.3198 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4729 Z= 0.105 Angle : 0.482 5.920 6434 Z= 0.247 Chirality : 0.038 0.150 760 Planarity : 0.003 0.024 792 Dihedral : 3.780 17.444 650 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.06 % Allowed : 12.45 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.07 (0.35), residues: 604 helix: 2.30 (0.30), residues: 293 sheet: 1.97 (0.52), residues: 105 loop : -0.33 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.011 0.001 TYR C 49 PHE 0.008 0.001 PHE A 72 TRP 0.008 0.001 TRP A 216 HIS 0.001 0.000 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4727) covalent geometry : angle 0.48240 / 0.25 ( 6430) SS BOND : bond 0.00221 / 0.11 ( 2) SS BOND : angle 0.26110 / 0.19 ( 4) hydrogen bonds : bond 0.03152 / 2.17 ( 285) hydrogen bonds : angle 4.58449 / 3.33 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8692 (tpp) cc_final: 0.8255 (tpp) REVERT: A 242 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6065 (mttt) REVERT: A 246 SER cc_start: 0.8619 (p) cc_final: 0.8227 (p) REVERT: A 379 TRP cc_start: 0.7377 (OUTLIER) cc_final: 0.6789 (m-10) REVERT: B 34 MET cc_start: 0.7303 (mtt) cc_final: 0.6552 (tpp) outliers start: 15 outliers final: 10 residues processed: 60 average time/residue: 0.0663 time to fit residues: 5.1282 Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.212349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150356 restraints weight = 5151.759| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.32 r_work: 0.3160 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4729 Z= 0.123 Angle : 0.495 5.873 6434 Z= 0.252 Chirality : 0.039 0.152 760 Planarity : 0.003 0.024 792 Dihedral : 3.793 17.442 650 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.06 % Allowed : 13.06 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.11 (0.35), residues: 604 helix: 2.28 (0.30), residues: 294 sheet: 2.07 (0.52), residues: 105 loop : -0.29 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.010 0.001 TYR C 49 PHE 0.010 0.001 PHE A 72 TRP 0.006 0.001 TRP A 216 HIS 0.002 0.000 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 ( 4727) covalent geometry : angle 0.49530 / 0.25 ( 6430) SS BOND : bond 0.00210 / 0.10 ( 2) SS BOND : angle 0.26903 / 0.21 ( 4) hydrogen bonds : bond 0.03354 / 2.31 ( 285) hydrogen bonds : angle 4.57676 / 3.34 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8705 (tpp) cc_final: 0.8287 (tpp) REVERT: A 242 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6105 (mttt) REVERT: A 245 ARG cc_start: 0.8044 (ttt180) cc_final: 0.7786 (ttt180) REVERT: A 379 TRP cc_start: 0.7462 (OUTLIER) cc_final: 0.6853 (m-10) REVERT: A 382 VAL cc_start: 0.8980 (m) cc_final: 0.8757 (p) REVERT: B 34 MET cc_start: 0.7234 (mtt) cc_final: 0.6710 (tpp) outliers start: 15 outliers final: 12 residues processed: 59 average time/residue: 0.0791 time to fit residues: 5.8628 Evaluate side-chains 63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 93 GLN A 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.212855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150812 restraints weight = 5155.355| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.30 r_work: 0.3405 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4729 Z= 0.111 Angle : 0.476 5.835 6434 Z= 0.243 Chirality : 0.038 0.151 760 Planarity : 0.003 0.025 792 Dihedral : 3.725 17.256 650 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.27 % Allowed : 13.06 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.19 (0.35), residues: 604 helix: 2.38 (0.30), residues: 290 sheet: 2.06 (0.51), residues: 105 loop : -0.23 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.010 0.001 TYR C 49 PHE 0.008 0.001 PHE A 72 TRP 0.008 0.001 TRP A 216 HIS 0.002 0.000 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 4727) covalent geometry : angle 0.47653 / 0.24 ( 6430) SS BOND : bond 0.00222 / 0.11 ( 2) SS BOND : angle 0.31270 / 0.26 ( 4) hydrogen bonds : bond 0.03157 / 2.18 ( 285) hydrogen bonds : angle 4.50153 / 3.28 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8744 (tpp) cc_final: 0.8389 (tpp) REVERT: A 242 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6413 (mttt) REVERT: A 245 ARG cc_start: 0.8105 (ttt180) cc_final: 0.7887 (ttt180) REVERT: A 379 TRP cc_start: 0.7546 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: A 382 VAL cc_start: 0.8968 (m) cc_final: 0.8736 (p) REVERT: B 34 MET cc_start: 0.7219 (mtt) cc_final: 0.6810 (tpp) outliers start: 16 outliers final: 14 residues processed: 62 average time/residue: 0.0918 time to fit residues: 7.1154 Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.213361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151575 restraints weight = 5100.880| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.27 r_work: 0.3202 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4729 Z= 0.097 Angle : 0.466 5.825 6434 Z= 0.237 Chirality : 0.038 0.151 760 Planarity : 0.003 0.025 792 Dihedral : 3.649 17.217 650 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.27 % Allowed : 13.67 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.27 (0.35), residues: 604 helix: 2.46 (0.30), residues: 290 sheet: 2.03 (0.52), residues: 105 loop : -0.18 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 383 TYR 0.009 0.001 TYR C 49 PHE 0.007 0.001 PHE A 72 TRP 0.008 0.001 TRP A 216 HIS 0.001 0.000 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 4727) covalent geometry : angle 0.46595 / 0.24 ( 6430) SS BOND : bond 0.00179 / 0.09 ( 2) SS BOND : angle 0.19961 / 0.16 ( 4) hydrogen bonds : bond 0.03052 / 2.10 ( 285) hydrogen bonds : angle 4.44320 / 3.24 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8662 (tpp) cc_final: 0.8283 (tpp) REVERT: A 242 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.5928 (mttt) REVERT: A 245 ARG cc_start: 0.8008 (ttt180) cc_final: 0.7780 (ttt180) REVERT: A 379 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.6794 (m-10) REVERT: A 382 VAL cc_start: 0.8964 (m) cc_final: 0.8727 (p) REVERT: B 34 MET cc_start: 0.7154 (mtt) cc_final: 0.6622 (tpp) outliers start: 16 outliers final: 14 residues processed: 61 average time/residue: 0.0872 time to fit residues: 6.6941 Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.0030 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.214488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.153283 restraints weight = 5141.268| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.27 r_work: 0.3224 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4729 Z= 0.091 Angle : 0.460 5.803 6434 Z= 0.235 Chirality : 0.037 0.150 760 Planarity : 0.003 0.025 792 Dihedral : 3.579 17.068 650 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.27 % Allowed : 13.67 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.41 (0.35), residues: 604 helix: 2.62 (0.30), residues: 288 sheet: 2.03 (0.52), residues: 105 loop : -0.09 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 381 TYR 0.009 0.001 TYR A 38 PHE 0.006 0.001 PHE A 72 TRP 0.008 0.001 TRP A 216 HIS 0.001 0.000 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 ( 4727) covalent geometry : angle 0.46012 / 0.23 ( 6430) SS BOND : bond 0.00201 / 0.10 ( 2) SS BOND : angle 0.29816 / 0.23 ( 4) hydrogen bonds : bond 0.02897 / 2.00 ( 285) hydrogen bonds : angle 4.37841 / 3.19 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 30 ASN cc_start: 0.8609 (m-40) cc_final: 0.8212 (t0) REVERT: A 59 MET cc_start: 0.8670 (tpp) cc_final: 0.8287 (tpp) REVERT: A 242 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.5965 (mttt) REVERT: A 245 ARG cc_start: 0.8002 (ttt180) cc_final: 0.7781 (ttt180) REVERT: A 246 SER cc_start: 0.8640 (p) cc_final: 0.8227 (p) REVERT: A 379 TRP cc_start: 0.7372 (OUTLIER) cc_final: 0.6722 (m-10) REVERT: A 382 VAL cc_start: 0.8965 (m) cc_final: 0.8728 (p) REVERT: B 34 MET cc_start: 0.7110 (mtt) cc_final: 0.6570 (tpp) outliers start: 16 outliers final: 14 residues processed: 65 average time/residue: 0.0889 time to fit residues: 7.2548 Evaluate side-chains 68 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 0.4980 chunk 54 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 40 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.213697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152657 restraints weight = 5165.218| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.32 r_work: 0.3209 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4729 Z= 0.101 Angle : 0.472 5.811 6434 Z= 0.239 Chirality : 0.038 0.150 760 Planarity : 0.003 0.024 792 Dihedral : 3.589 17.033 650 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.06 % Allowed : 14.08 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.42 (0.35), residues: 604 helix: 2.61 (0.30), residues: 288 sheet: 2.04 (0.52), residues: 105 loop : -0.06 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 381 TYR 0.009 0.001 TYR C 49 PHE 0.008 0.001 PHE A 72 TRP 0.008 0.001 TRP A 216 HIS 0.001 0.000 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 4727) covalent geometry : angle 0.47186 / 0.24 ( 6430) SS BOND : bond 0.00193 / 0.09 ( 2) SS BOND : angle 0.27934 / 0.22 ( 4) hydrogen bonds : bond 0.02979 / 2.06 ( 285) hydrogen bonds : angle 4.39445 / 3.20 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.41 seconds wall clock time: 24 minutes 46.05 seconds (1486.05 seconds total)