Starting phenix.real_space_refine on Thu Jul 2 02:51:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zq9_60379/07_2026/8zq9_60379_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zq9_60379/07_2026/8zq9_60379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zq9_60379/07_2026/8zq9_60379_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zq9_60379/07_2026/8zq9_60379_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zq9_60379/07_2026/8zq9_60379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zq9_60379/07_2026/8zq9_60379.map" } resolution = 2.87 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= -0.001 sd= 0.054 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 125 5.49 5 S 14 5.16 5 C 3419 2.51 5 N 1124 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6211 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2653 Classifications: {'RNA': 125} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 12, 'rna3p_pur': 53, 'rna3p_pyr': 53} Link IDs: {'rna2p': 19, 'rna3p': 105} Chain breaks: 2 Chain: "B" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3557 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 425} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4038 SG CYS B 182 40.779 31.073 78.743 1.00 30.00 S ATOM 4077 SG CYS B 187 43.337 28.201 79.182 1.00 30.00 S ATOM 4701 SG CYS B 264 39.812 27.494 77.732 1.00 65.90 S Time building chain proxies: 1.41, per 1000 atoms: 0.23 Number of scatterers: 6211 At special positions: 0 Unit cell: (73.87, 97.94, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 14 16.00 P 125 15.00 O 1528 8.00 N 1124 7.00 C 3419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.52 Conformation dependent library (CDL) restraints added in 243.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 267 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 182 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 264 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 187 " Number of angles added : 3 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 53.3% alpha, 8.8% beta 33 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'B' and resid 39 through 74 Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.680A pdb=" N THR B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 91 " --> pdb=" O TYR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 133 removed outlier: 3.553A pdb=" N ASN B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 150 removed outlier: 3.660A pdb=" N VAL B 140 " --> pdb=" O HIS B 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.530A pdb=" N ARG B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 207 removed outlier: 3.615A pdb=" N GLU B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 228 through 239 removed outlier: 3.712A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 285 through 304 Processing helix chain 'B' and resid 449 through 462 Processing helix chain 'B' and resid 474 through 485 removed outlier: 3.509A pdb=" N THR B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 Processing helix chain 'B' and resid 579 through 583 removed outlier: 3.620A pdb=" N ASP B 582 " --> pdb=" O LYS B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 599 removed outlier: 4.472A pdb=" N GLU B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 35 removed outlier: 5.149A pdb=" N VAL B 28 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP B 22 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 5 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL B 312 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 7 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N MET B 314 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 9 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 561 through 562 removed outlier: 3.862A pdb=" N LYS B 562 " --> pdb=" O ILE B 565 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1297 1.33 - 1.45: 2068 1.45 - 1.57: 2935 1.57 - 1.69: 247 1.69 - 1.81: 22 Bond restraints: 6569 Sorted by residual: bond pdb=" C ARG B 137 " pdb=" N LYS B 138 " ideal model delta sigma weight residual 1.335 1.246 0.089 1.31e-02 5.83e+03 4.62e+01 bond pdb=" C ARG B 491 " pdb=" N GLY B 492 " ideal model delta sigma weight residual 1.329 1.244 0.085 1.36e-02 5.41e+03 3.93e+01 bond pdb=" C SER B 560 " pdb=" N TYR B 561 " ideal model delta sigma weight residual 1.330 1.254 0.076 1.36e-02 5.41e+03 3.13e+01 bond pdb=" C ASN B 310 " pdb=" N LYS B 311 " ideal model delta sigma weight residual 1.332 1.265 0.066 1.26e-02 6.30e+03 2.78e+01 bond pdb=" C GLU B 490 " pdb=" N ARG B 491 " ideal model delta sigma weight residual 1.331 1.263 0.067 1.42e-02 4.96e+03 2.25e+01 ... (remaining 6564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 8562 1.76 - 3.53: 657 3.53 - 5.29: 121 5.29 - 7.05: 82 7.05 - 8.82: 8 Bond angle restraints: 9430 Sorted by residual: angle pdb=" C ARG B 137 " pdb=" N LYS B 138 " pdb=" CA LYS B 138 " ideal model delta sigma weight residual 120.28 127.61 -7.33 1.34e+00 5.57e-01 2.99e+01 angle pdb=" O3' G A 107 " pdb=" C3' G A 107 " pdb=" C2' G A 107 " ideal model delta sigma weight residual 113.70 105.97 7.73 1.50e+00 4.44e-01 2.66e+01 angle pdb=" O3' C A 129 " pdb=" P U A 130 " pdb=" O5' U A 130 " ideal model delta sigma weight residual 104.00 96.89 7.11 1.50e+00 4.44e-01 2.25e+01 angle pdb=" C1' U A 81 " pdb=" N1 U A 81 " pdb=" C2 U A 81 " ideal model delta sigma weight residual 117.70 123.21 -5.51 1.20e+00 6.94e-01 2.11e+01 angle pdb=" O3' U A 114 " pdb=" P G A 115 " pdb=" O5' G A 115 " ideal model delta sigma weight residual 104.00 97.20 6.80 1.50e+00 4.44e-01 2.06e+01 ... (remaining 9425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 3757 35.84 - 71.68: 370 71.68 - 107.52: 46 107.52 - 143.36: 1 143.36 - 179.21: 6 Dihedral angle restraints: 4180 sinusoidal: 2911 harmonic: 1269 Sorted by residual: dihedral pdb=" O4' U A 81 " pdb=" C1' U A 81 " pdb=" N1 U A 81 " pdb=" C2 U A 81 " ideal model delta sinusoidal sigma weight residual 200.00 43.24 156.76 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" O4' C A 15 " pdb=" C1' C A 15 " pdb=" N1 C A 15 " pdb=" C2 C A 15 " ideal model delta sinusoidal sigma weight residual -128.00 51.21 -179.21 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 94 " pdb=" C1' U A 94 " pdb=" N1 U A 94 " pdb=" C2 U A 94 " ideal model delta sinusoidal sigma weight residual -128.00 36.10 -164.10 1 1.70e+01 3.46e-03 6.52e+01 ... (remaining 4177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1000 0.108 - 0.216: 104 0.216 - 0.324: 3 0.324 - 0.432: 10 0.432 - 0.540: 32 Chirality restraints: 1149 Sorted by residual: chirality pdb=" P C A 49 " pdb=" OP1 C A 49 " pdb=" OP2 C A 49 " pdb=" O5' C A 49 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" P U A 110 " pdb=" OP1 U A 110 " pdb=" OP2 U A 110 " pdb=" O5' U A 110 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" P G A 124 " pdb=" OP1 G A 124 " pdb=" OP2 G A 124 " pdb=" O5' G A 124 " both_signs ideal model delta sigma weight residual True 2.41 2.93 -0.52 2.00e-01 2.50e+01 6.72e+00 ... (remaining 1146 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 137 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C ARG B 137 " -0.047 2.00e-02 2.50e+03 pdb=" O ARG B 137 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS B 138 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 144 " 0.033 2.00e-02 2.50e+03 1.40e-02 5.89e+00 pdb=" N9 G A 144 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G A 144 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 144 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 144 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 144 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 144 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G A 144 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G A 144 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G A 144 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G A 144 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G A 144 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 218 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" CG ASN B 218 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 218 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 218 " 0.014 2.00e-02 2.50e+03 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1487 2.80 - 3.32: 5619 3.32 - 3.85: 12162 3.85 - 4.37: 14031 4.37 - 4.90: 20245 Nonbonded interactions: 53544 Sorted by model distance: nonbonded pdb=" O2' U A 24 " pdb=" O PRO B 558 " model vdw 2.272 3.040 nonbonded pdb=" NZ LYS B 181 " pdb=" OD1 ASN B 190 " model vdw 2.305 3.120 nonbonded pdb=" NH2 ARG B 63 " pdb=" O LYS B 167 " model vdw 2.314 3.120 nonbonded pdb=" O2' C A 64 " pdb=" OP1 U A 93 " model vdw 2.330 3.040 nonbonded pdb=" OP1 U A 18 " pdb=" NE ARG B 170 " model vdw 2.331 3.120 ... (remaining 53539 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: 0.010 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.260 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 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 : 0.007 0.089 6573 Z= 0.507 Angle : 1.130 8.818 9433 Z= 0.751 Chirality : 0.106 0.540 1149 Planarity : 0.006 0.091 740 Dihedral : 23.706 179.205 3352 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.11 % Allowed : 25.86 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.39), residues: 417 helix: -0.40 (0.34), residues: 212 sheet: -1.07 (0.76), residues: 40 loop : -2.59 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 207 TYR 0.012 0.001 TYR B 561 PHE 0.029 0.002 PHE B 487 TRP 0.007 0.002 TRP B 452 HIS 0.003 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.51 ( 6569) covalent geometry : angle 1.12962 / 0.75 ( 9430) hydrogen bonds : bond 0.17627 / 17.14 ( 250) hydrogen bonds : angle 7.26381 / 8.32 ( 633) metal coordination : bond 0.00414 / 0.24 ( 4) metal coordination : angle 1.02258 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: B 163 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7189 (mtm110) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.5665 time to fit residues: 32.0648 Evaluate side-chains 42 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.186622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.153050 restraints weight = 8131.695| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.41 r_work: 0.3760 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6573 Z= 0.203 Angle : 0.629 8.463 9433 Z= 0.366 Chirality : 0.042 0.257 1149 Planarity : 0.005 0.060 740 Dihedral : 24.044 175.524 2438 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.96 % Allowed : 27.44 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.32 (0.39), residues: 417 helix: 0.32 (0.35), residues: 217 sheet: -0.40 (0.75), residues: 40 loop : -2.73 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 207 TYR 0.011 0.001 TYR B 169 PHE 0.026 0.002 PHE B 487 TRP 0.007 0.002 TRP B 452 HIS 0.006 0.002 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 ( 6569) covalent geometry : angle 0.62788 / 0.37 ( 9430) hydrogen bonds : bond 0.06160 / 6.26 ( 250) hydrogen bonds : angle 4.36844 / 5.07 ( 633) metal coordination : bond 0.00453 / 0.28 ( 4) metal coordination : angle 1.78601 / 3.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: B 47 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.6995 (mtp-110) REVERT: B 162 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: B 313 VAL cc_start: 0.8050 (t) cc_final: 0.7794 (t) REVERT: B 314 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.5926 (tmt) REVERT: B 503 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7437 (mt) outliers start: 15 outliers final: 8 residues processed: 53 average time/residue: 0.5743 time to fit residues: 31.9186 Evaluate side-chains 51 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.0170 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.188528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154593 restraints weight = 7946.806| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.38 r_work: 0.3785 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6573 Z= 0.134 Angle : 0.541 8.389 9433 Z= 0.316 Chirality : 0.037 0.207 1149 Planarity : 0.004 0.056 740 Dihedral : 23.910 178.328 2435 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.28 % Allowed : 26.12 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.41), residues: 417 helix: 0.69 (0.35), residues: 220 sheet: 0.05 (0.78), residues: 39 loop : -2.57 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 207 TYR 0.007 0.001 TYR B 70 PHE 0.021 0.002 PHE B 263 TRP 0.009 0.001 TRP B 452 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 6569) covalent geometry : angle 0.54058 / 0.32 ( 9430) hydrogen bonds : bond 0.04871 / 5.00 ( 250) hydrogen bonds : angle 4.01166 / 4.69 ( 633) metal coordination : bond 0.01162 / 0.77 ( 4) metal coordination : angle 1.16717 / 2.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: B 47 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7060 (mtp180) REVERT: B 132 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.5963 (ttm110) REVERT: B 162 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: B 180 THR cc_start: 0.6835 (p) cc_final: 0.6470 (t) REVERT: B 459 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7062 (tt) REVERT: B 503 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7391 (mt) outliers start: 20 outliers final: 6 residues processed: 58 average time/residue: 0.5191 time to fit residues: 31.6264 Evaluate side-chains 51 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 ASN B 496 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.186432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.151915 restraints weight = 8045.100| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.43 r_work: 0.3759 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6573 Z= 0.150 Angle : 0.541 9.004 9433 Z= 0.313 Chirality : 0.038 0.190 1149 Planarity : 0.004 0.058 740 Dihedral : 23.751 177.163 2432 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.01 % Allowed : 27.18 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.41), residues: 417 helix: 0.81 (0.36), residues: 224 sheet: 0.28 (0.77), residues: 39 loop : -2.67 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 207 TYR 0.011 0.001 TYR B 169 PHE 0.025 0.002 PHE B 263 TRP 0.005 0.001 TRP B 452 HIS 0.004 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 6569) covalent geometry : angle 0.54057 / 0.31 ( 9430) hydrogen bonds : bond 0.04889 / 4.91 ( 250) hydrogen bonds : angle 3.81811 / 4.54 ( 633) metal coordination : bond 0.00595 / 0.34 ( 4) metal coordination : angle 1.13284 / 2.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 47 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.6956 (mtp-110) REVERT: B 132 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6135 (ttm110) REVERT: B 162 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: B 180 THR cc_start: 0.6936 (p) cc_final: 0.6620 (t) REVERT: B 314 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6060 (tmm) REVERT: B 503 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7445 (mt) outliers start: 19 outliers final: 9 residues processed: 57 average time/residue: 0.6264 time to fit residues: 37.3310 Evaluate side-chains 53 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN B 218 ASN B 497 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.180390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145667 restraints weight = 8196.319| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.61 r_work: 0.3663 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6573 Z= 0.254 Angle : 0.651 9.394 9433 Z= 0.368 Chirality : 0.044 0.223 1149 Planarity : 0.006 0.062 740 Dihedral : 23.735 173.675 2432 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.33 % Allowed : 26.39 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.11 (0.40), residues: 417 helix: 0.37 (0.35), residues: 224 sheet: 0.18 (0.75), residues: 39 loop : -2.70 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 283 TYR 0.019 0.002 TYR B 169 PHE 0.033 0.003 PHE B 263 TRP 0.009 0.002 TRP B 452 HIS 0.007 0.002 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.25 ( 6569) covalent geometry : angle 0.64986 / 0.37 ( 9430) hydrogen bonds : bond 0.06302 / 6.11 ( 250) hydrogen bonds : angle 3.98379 / 4.72 ( 633) metal coordination : bond 0.01268 / 0.67 ( 4) metal coordination : angle 2.00749 / 1.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 44 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7698 (mp) REVERT: B 47 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7070 (ttp-110) REVERT: B 132 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6396 (ttm110) REVERT: B 133 ASN cc_start: 0.8229 (p0) cc_final: 0.8011 (p0) REVERT: B 162 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: B 314 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6612 (tmt) outliers start: 24 outliers final: 14 residues processed: 65 average time/residue: 0.4643 time to fit residues: 31.8310 Evaluate side-chains 64 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 485 TRP Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 53 optimal weight: 0.0770 chunk 35 optimal weight: 0.0570 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.185032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.150651 restraints weight = 8124.338| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.51 r_work: 0.3737 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6573 Z= 0.127 Angle : 0.525 9.608 9433 Z= 0.306 Chirality : 0.037 0.206 1149 Planarity : 0.004 0.056 740 Dihedral : 23.698 179.094 2432 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.75 % Allowed : 28.23 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.51 (0.42), residues: 417 helix: 0.87 (0.36), residues: 220 sheet: 0.47 (0.77), residues: 39 loop : -2.36 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 246 TYR 0.008 0.001 TYR B 169 PHE 0.025 0.002 PHE B 263 TRP 0.011 0.001 TRP B 484 HIS 0.002 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 ( 6569) covalent geometry : angle 0.52463 / 0.31 ( 9430) hydrogen bonds : bond 0.04618 / 4.57 ( 250) hydrogen bonds : angle 3.76306 / 4.40 ( 633) metal coordination : bond 0.00843 / 0.55 ( 4) metal coordination : angle 1.71077 / 3.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.190 Fit side-chains REVERT: B 44 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7616 (mp) REVERT: B 47 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7101 (mtp180) REVERT: B 132 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6313 (ttm110) REVERT: B 162 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: B 180 THR cc_start: 0.7185 (p) cc_final: 0.6889 (t) REVERT: B 314 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6433 (tmm) outliers start: 18 outliers final: 7 residues processed: 53 average time/residue: 0.5794 time to fit residues: 32.2196 Evaluate side-chains 52 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.179728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145533 restraints weight = 8173.331| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.61 r_work: 0.3660 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 6573 Z= 0.265 Angle : 0.655 9.855 9433 Z= 0.367 Chirality : 0.043 0.222 1149 Planarity : 0.006 0.059 740 Dihedral : 23.625 174.134 2432 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.86 % Allowed : 26.65 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.41), residues: 417 helix: 0.39 (0.35), residues: 224 sheet: 0.55 (0.78), residues: 39 loop : -2.61 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 283 TYR 0.017 0.002 TYR B 169 PHE 0.033 0.003 PHE B 263 TRP 0.013 0.002 TRP B 484 HIS 0.004 0.001 HIS B 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.27 ( 6569) covalent geometry : angle 0.65397 / 0.37 ( 9430) hydrogen bonds : bond 0.06202 / 5.99 ( 250) hydrogen bonds : angle 3.95013 / 4.62 ( 633) metal coordination : bond 0.01316 / 0.70 ( 4) metal coordination : angle 2.18750 / 1.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.181 Fit side-chains REVERT: B 44 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7716 (mp) REVERT: B 47 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7085 (ttp-110) REVERT: B 132 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6620 (ttm110) REVERT: B 162 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: B 180 THR cc_start: 0.7624 (p) cc_final: 0.7360 (t) REVERT: B 283 ARG cc_start: 0.7725 (mtp-110) cc_final: 0.7520 (mtm110) REVERT: B 314 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6762 (tmt) REVERT: B 503 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7719 (mt) REVERT: B 596 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6482 (m-10) outliers start: 26 outliers final: 12 residues processed: 62 average time/residue: 0.5332 time to fit residues: 34.6585 Evaluate side-chains 58 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 485 TRP Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.184168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.149541 restraints weight = 8175.586| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.49 r_work: 0.3724 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6573 Z= 0.129 Angle : 0.528 9.929 9433 Z= 0.306 Chirality : 0.037 0.212 1149 Planarity : 0.004 0.055 740 Dihedral : 23.566 178.734 2432 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.07 % Allowed : 27.97 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.57 (0.42), residues: 417 helix: 0.77 (0.36), residues: 224 sheet: 0.82 (0.79), residues: 39 loop : -2.51 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 207 TYR 0.009 0.001 TYR B 169 PHE 0.025 0.002 PHE B 263 TRP 0.011 0.001 TRP B 484 HIS 0.002 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 6569) covalent geometry : angle 0.52727 / 0.31 ( 9430) hydrogen bonds : bond 0.04583 / 4.42 ( 250) hydrogen bonds : angle 3.74540 / 4.38 ( 633) metal coordination : bond 0.00647 / 0.42 ( 4) metal coordination : angle 1.43653 / 3.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.107 Fit side-chains REVERT: B 44 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7617 (mp) REVERT: B 47 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7075 (mtp180) REVERT: B 132 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6433 (ttm110) REVERT: B 162 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: B 168 GLN cc_start: 0.8612 (tp-100) cc_final: 0.7801 (tp-100) REVERT: B 180 THR cc_start: 0.7349 (p) cc_final: 0.7080 (t) REVERT: B 207 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7392 (mtm-85) REVERT: B 503 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7640 (mt) REVERT: B 596 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6383 (m-10) outliers start: 23 outliers final: 10 residues processed: 57 average time/residue: 0.5373 time to fit residues: 32.0422 Evaluate side-chains 55 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 485 TRP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 9.9990 chunk 53 optimal weight: 0.0470 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.0070 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN B 133 ASN B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.187240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.153678 restraints weight = 8182.277| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.47 r_work: 0.3778 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6573 Z= 0.115 Angle : 0.502 10.106 9433 Z= 0.289 Chirality : 0.035 0.213 1149 Planarity : 0.004 0.050 740 Dihedral : 23.393 179.809 2432 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.80 % Favored : 94.96 % Rotamer: Outliers : 4.49 % Allowed : 29.55 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.42), residues: 417 helix: 1.17 (0.36), residues: 220 sheet: 1.23 (0.79), residues: 37 loop : -2.11 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 207 TYR 0.008 0.001 TYR B 169 PHE 0.021 0.002 PHE B 263 TRP 0.015 0.002 TRP B 452 HIS 0.002 0.000 HIS B 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 ( 6569) covalent geometry : angle 0.50175 / 0.29 ( 9430) hydrogen bonds : bond 0.04073 / 3.94 ( 250) hydrogen bonds : angle 3.58094 / 4.22 ( 633) metal coordination : bond 0.00476 / 0.31 ( 4) metal coordination : angle 1.25192 / 1.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.165 Fit side-chains REVERT: B 33 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.5702 (ptm-80) REVERT: B 44 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7519 (mp) REVERT: B 132 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6224 (ttm110) REVERT: B 133 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7255 (p0) REVERT: B 162 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: B 180 THR cc_start: 0.7100 (p) cc_final: 0.6744 (t) outliers start: 17 outliers final: 7 residues processed: 57 average time/residue: 0.5906 time to fit residues: 35.1899 Evaluate side-chains 50 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN B 133 ASN B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.186428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152751 restraints weight = 8177.510| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.38 r_work: 0.3777 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6573 Z= 0.130 Angle : 0.518 10.083 9433 Z= 0.297 Chirality : 0.036 0.212 1149 Planarity : 0.004 0.053 740 Dihedral : 23.352 178.738 2432 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.80 % Favored : 94.96 % Rotamer: Outliers : 3.69 % Allowed : 31.40 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.42), residues: 417 helix: 1.24 (0.36), residues: 220 sheet: 1.21 (0.79), residues: 37 loop : -2.09 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 135 TYR 0.009 0.001 TYR B 169 PHE 0.022 0.002 PHE B 263 TRP 0.013 0.002 TRP B 452 HIS 0.004 0.001 HIS B 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 6569) covalent geometry : angle 0.51785 / 0.30 ( 9430) hydrogen bonds : bond 0.04265 / 4.14 ( 250) hydrogen bonds : angle 3.59620 / 4.24 ( 633) metal coordination : bond 0.00335 / 0.19 ( 4) metal coordination : angle 0.63058 / 0.55 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.147 Fit side-chains REVERT: B 44 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7516 (mp) REVERT: B 132 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6220 (ttm110) REVERT: B 133 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.7130 (p0) REVERT: B 162 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: B 180 THR cc_start: 0.7083 (p) cc_final: 0.6795 (t) REVERT: B 503 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7556 (mt) outliers start: 14 outliers final: 9 residues processed: 48 average time/residue: 0.4792 time to fit residues: 24.2890 Evaluate side-chains 52 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.186412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.152701 restraints weight = 8118.959| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.38 r_work: 0.3776 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 6573 Z= 0.167 Angle : 0.928 59.194 9433 Z= 0.554 Chirality : 0.036 0.212 1149 Planarity : 0.004 0.052 740 Dihedral : 23.353 178.703 2432 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.80 % Favored : 94.96 % Rotamer: Outliers : 4.49 % Allowed : 30.61 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.42), residues: 417 helix: 1.24 (0.36), residues: 220 sheet: 1.22 (0.78), residues: 37 loop : -2.09 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.008 0.001 TYR B 169 PHE 0.022 0.002 PHE B 263 TRP 0.013 0.002 TRP B 484 HIS 0.002 0.001 HIS B 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 ( 6569) covalent geometry : angle 0.92832 / 0.55 ( 9430) hydrogen bonds : bond 0.04273 / 4.14 ( 250) hydrogen bonds : angle 3.59880 / 4.24 ( 633) metal coordination : bond 0.00362 / 0.20 ( 4) metal coordination : angle 0.63103 / 0.56 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2151.46 seconds wall clock time: 37 minutes 30.67 seconds (2250.67 seconds total)