Starting phenix.real_space_refine on Sat May 10 11:14:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zq9_60379/05_2025/8zq9_60379_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zq9_60379/05_2025/8zq9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zq9_60379/05_2025/8zq9_60379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zq9_60379/05_2025/8zq9_60379.map" model { file = "/net/cci-nas-00/data/ceres_data/8zq9_60379/05_2025/8zq9_60379_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zq9_60379/05_2025/8zq9_60379_neut.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'GLU:plan': 1, 'ARG:plan': 3, '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: 4.71, per 1000 atoms: 0.76 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: 1.62 Conformation dependent library (CDL) restraints added in 595.4 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: 2.83 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: 2.56 Time building geometry restraints manager: 1.87 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=" 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 angle pdb=" O SER B 560 " pdb=" C SER B 560 " pdb=" N TYR B 561 " ideal model delta sigma weight residual 123.10 117.94 5.16 1.15e+00 7.56e-01 2.01e+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: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.810 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 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= 0.486 Angle : 1.129 8.818 9433 Z= 0.663 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.002 TRP B 452 HIS 0.003 0.001 HIS B 274 PHE 0.029 0.002 PHE B 487 TYR 0.012 0.001 TYR B 561 ARG 0.010 0.001 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.17627 ( 250) hydrogen bonds : angle 7.26381 ( 633) metal coordination : bond 0.00414 ( 4) metal coordination : angle 1.02258 ( 3) covalent geometry : bond 0.00745 ( 6569) covalent geometry : angle 1.12953 ( 9430) *********************** 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 : 0.524 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: 1.2315 time to fit residues: 69.9217 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 : 0.510 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.188531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154583 restraints weight = 7956.945| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.38 r_work: 0.3788 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6573 Z= 0.155 Angle : 0.637 9.812 9433 Z= 0.326 Chirality : 0.037 0.214 1149 Planarity : 0.004 0.069 740 Dihedral : 23.794 175.738 2438 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.17 % Allowed : 27.18 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.40), residues: 417 helix: 0.64 (0.35), residues: 217 sheet: -0.18 (0.77), residues: 39 loop : -2.68 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 452 HIS 0.002 0.001 HIS B 274 PHE 0.024 0.002 PHE B 263 TYR 0.008 0.001 TYR B 70 ARG 0.005 0.001 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 250) hydrogen bonds : angle 4.15292 ( 633) metal coordination : bond 0.01333 ( 4) metal coordination : angle 1.33843 ( 3) covalent geometry : bond 0.00310 ( 6569) covalent geometry : angle 0.63654 ( 9430) *********************** 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 54 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: B 47 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6926 (mtp-110) REVERT: B 162 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7060 (mt-10) REVERT: B 180 THR cc_start: 0.6846 (p) cc_final: 0.6513 (t) REVERT: B 283 ARG cc_start: 0.7232 (mtp-110) cc_final: 0.6672 (ppt170) REVERT: B 503 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7418 (mt) outliers start: 12 outliers final: 5 residues processed: 51 average time/residue: 1.3590 time to fit residues: 72.5882 Evaluate side-chains 43 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 303 ILE 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 49 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4252 r_free = 0.4252 target = 0.181112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142476 restraints weight = 8079.636| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.32 r_work: 0.3696 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 6573 Z= 0.230 Angle : 0.711 9.353 9433 Z= 0.359 Chirality : 0.040 0.200 1149 Planarity : 0.005 0.066 740 Dihedral : 23.688 172.447 2432 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.80 % Allowed : 24.80 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.40), residues: 417 helix: 0.43 (0.35), residues: 224 sheet: -0.13 (0.73), residues: 39 loop : -2.75 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 452 HIS 0.005 0.001 HIS B 497 PHE 0.031 0.002 PHE B 263 TYR 0.013 0.002 TYR B 169 ARG 0.004 0.001 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 250) hydrogen bonds : angle 4.00066 ( 633) metal coordination : bond 0.01221 ( 4) metal coordination : angle 2.20013 ( 3) covalent geometry : bond 0.00471 ( 6569) covalent geometry : angle 0.71012 ( 9430) *********************** 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 64 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.478 Fit side-chains REVERT: B 47 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7037 (mtp-110) REVERT: B 162 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7231 (mt-10) outliers start: 22 outliers final: 9 residues processed: 57 average time/residue: 1.1649 time to fit residues: 70.0156 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 : 0.497 ------------------------------------------------------------------------------- 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 261 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 303 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.182267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.147784 restraints weight = 8156.012| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.44 r_work: 0.3708 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6573 Z= 0.192 Angle : 0.651 9.848 9433 Z= 0.325 Chirality : 0.038 0.208 1149 Planarity : 0.004 0.060 740 Dihedral : 23.442 175.238 2432 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.07 % Allowed : 26.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.41), residues: 417 helix: 0.55 (0.35), residues: 224 sheet: 0.48 (0.77), residues: 37 loop : -2.43 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 484 HIS 0.004 0.001 HIS B 497 PHE 0.029 0.003 PHE B 263 TYR 0.010 0.001 TYR B 169 ARG 0.006 0.001 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04837 ( 250) hydrogen bonds : angle 3.85002 ( 633) metal coordination : bond 0.00813 ( 4) metal coordination : angle 1.35196 ( 3) covalent geometry : bond 0.00387 ( 6569) covalent geometry : angle 0.65039 ( 9430) *********************** 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 68 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.478 Fit side-chains REVERT: B 44 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 47 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7032 (ttp-110) REVERT: B 132 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6414 (ttm110) REVERT: B 162 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: B 307 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6598 (m-80) outliers start: 23 outliers final: 8 residues processed: 60 average time/residue: 1.2906 time to fit residues: 81.0546 Evaluate side-chains 53 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 208 PHE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 307 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.183834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145894 restraints weight = 8132.731| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.29 r_work: 0.3748 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6573 Z= 0.160 Angle : 0.617 10.060 9433 Z= 0.310 Chirality : 0.036 0.213 1149 Planarity : 0.004 0.056 740 Dihedral : 23.369 176.416 2432 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.33 % Allowed : 26.91 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.41), residues: 417 helix: 0.70 (0.35), residues: 224 sheet: 0.82 (0.79), residues: 37 loop : -2.39 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 484 HIS 0.003 0.001 HIS B 497 PHE 0.024 0.002 PHE B 263 TYR 0.009 0.001 TYR B 169 ARG 0.008 0.001 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 250) hydrogen bonds : angle 3.71255 ( 633) metal coordination : bond 0.00696 ( 4) metal coordination : angle 1.74557 ( 3) covalent geometry : bond 0.00322 ( 6569) covalent geometry : angle 0.61605 ( 9430) *********************** 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 65 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.596 Fit side-chains REVERT: B 44 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7518 (mp) REVERT: B 47 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7015 (mtp-110) REVERT: B 132 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6469 (tmm160) REVERT: B 162 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: B 168 GLN cc_start: 0.8555 (tp-100) cc_final: 0.7833 (tp-100) REVERT: B 314 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6504 (tmm) REVERT: B 503 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7579 (mt) outliers start: 24 outliers final: 10 residues processed: 57 average time/residue: 1.4328 time to fit residues: 85.3631 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 : 0.492 ------------------------------------------------------------------------------- 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 258 SER Chi-restraints excluded: chain B residue 262 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 518 MET 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 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4291 r_free = 0.4291 target = 0.185368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151097 restraints weight = 8060.197| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.40 r_work: 0.3750 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6573 Z= 0.143 Angle : 0.596 10.109 9433 Z= 0.298 Chirality : 0.035 0.210 1149 Planarity : 0.004 0.054 740 Dihedral : 23.317 177.127 2432 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.07 % Allowed : 28.50 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.42), residues: 417 helix: 0.88 (0.36), residues: 224 sheet: 1.22 (0.82), residues: 37 loop : -2.34 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 452 HIS 0.002 0.001 HIS B 497 PHE 0.024 0.002 PHE B 263 TYR 0.008 0.001 TYR B 169 ARG 0.009 0.001 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 250) hydrogen bonds : angle 3.57097 ( 633) metal coordination : bond 0.00415 ( 4) metal coordination : angle 0.95554 ( 3) covalent geometry : bond 0.00286 ( 6569) covalent geometry : angle 0.59569 ( 9430) *********************** 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 68 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.508 Fit side-chains REVERT: B 44 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7681 (mp) REVERT: B 47 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7058 (mtp180) REVERT: B 132 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6292 (tmm160) REVERT: B 162 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: B 452 TRP cc_start: 0.6583 (OUTLIER) cc_final: 0.5319 (t-100) REVERT: B 596 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6339 (m-10) outliers start: 23 outliers final: 9 residues processed: 60 average time/residue: 1.2418 time to fit residues: 78.2528 Evaluate side-chains 54 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 33 ARG 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 262 VAL Chi-restraints excluded: chain B residue 452 TRP 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 596 PHE 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 9 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 21 optimal weight: 0.0030 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.0060 chunk 30 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4344 r_free = 0.4344 target = 0.190198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157068 restraints weight = 8102.274| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.38 r_work: 0.3827 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6573 Z= 0.108 Angle : 0.560 9.789 9433 Z= 0.279 Chirality : 0.033 0.201 1149 Planarity : 0.004 0.051 740 Dihedral : 23.200 179.617 2432 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.04 % Favored : 94.72 % Rotamer: Outliers : 5.01 % Allowed : 29.82 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.42), residues: 417 helix: 1.30 (0.36), residues: 221 sheet: 1.40 (0.82), residues: 37 loop : -2.39 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 452 HIS 0.002 0.001 HIS B 496 PHE 0.020 0.002 PHE B 235 TYR 0.004 0.001 TYR B 70 ARG 0.006 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 250) hydrogen bonds : angle 3.45173 ( 633) metal coordination : bond 0.00299 ( 4) metal coordination : angle 0.97925 ( 3) covalent geometry : bond 0.00219 ( 6569) covalent geometry : angle 0.55998 ( 9430) *********************** 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 61 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.529 Fit side-chains REVERT: B 33 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.5707 (ptm-80) REVERT: B 44 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7571 (mp) REVERT: B 47 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7210 (mtp180) REVERT: B 132 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6220 (tmm160) REVERT: B 168 GLN cc_start: 0.8414 (tp-100) cc_final: 0.7685 (tp-100) REVERT: B 307 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6301 (m-80) REVERT: B 452 TRP cc_start: 0.6635 (OUTLIER) cc_final: 0.5391 (t-100) REVERT: B 491 ARG cc_start: 0.6510 (ttm170) cc_final: 0.6262 (mtt180) outliers start: 19 outliers final: 6 residues processed: 54 average time/residue: 1.3809 time to fit residues: 78.0756 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 : 0.503 ------------------------------------------------------------------------------- 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 33 ARG 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 273 GLU Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 567 THR 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 1 optimal weight: 4.9990 chunk 23 optimal weight: 0.0370 chunk 10 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.186247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.152394 restraints weight = 7996.630| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.38 r_work: 0.3766 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6573 Z= 0.147 Angle : 0.591 9.262 9433 Z= 0.294 Chirality : 0.035 0.190 1149 Planarity : 0.004 0.051 740 Dihedral : 23.162 176.381 2432 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.56 % Favored : 95.20 % Rotamer: Outliers : 5.28 % Allowed : 30.34 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.42), residues: 417 helix: 1.23 (0.36), residues: 224 sheet: 1.32 (0.82), residues: 37 loop : -2.36 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 452 HIS 0.002 0.001 HIS B 497 PHE 0.023 0.002 PHE B 263 TYR 0.009 0.001 TYR B 169 ARG 0.006 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 250) hydrogen bonds : angle 3.45418 ( 633) metal coordination : bond 0.00553 ( 4) metal coordination : angle 0.89382 ( 3) covalent geometry : bond 0.00298 ( 6569) covalent geometry : angle 0.59098 ( 9430) *********************** 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 62 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.484 Fit side-chains REVERT: B 44 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7654 (mp) REVERT: B 47 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.6953 (mtp-110) REVERT: B 132 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6303 (tmm160) REVERT: B 452 TRP cc_start: 0.6652 (OUTLIER) cc_final: 0.5385 (t-100) REVERT: B 491 ARG cc_start: 0.6520 (ttm170) cc_final: 0.6283 (mtt180) REVERT: B 503 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7639 (mt) REVERT: B 557 ASN cc_start: 0.8080 (m-40) cc_final: 0.7874 (m110) REVERT: B 596 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6422 (m-10) outliers start: 20 outliers final: 11 residues processed: 56 average time/residue: 1.2278 time to fit residues: 72.2983 Evaluate side-chains 56 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 16 THR 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 47 ARG Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 452 TRP 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 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 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 41 optimal weight: 0.0980 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4262 r_free = 0.4262 target = 0.182525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.147842 restraints weight = 8133.066| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.46 r_work: 0.3705 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6573 Z= 0.200 Angle : 0.654 8.364 9433 Z= 0.327 Chirality : 0.038 0.173 1149 Planarity : 0.004 0.052 740 Dihedral : 23.192 174.250 2432 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.75 % Allowed : 30.61 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.42), residues: 417 helix: 0.98 (0.35), residues: 222 sheet: 0.99 (0.80), residues: 38 loop : -2.40 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 484 HIS 0.004 0.001 HIS B 497 PHE 0.030 0.003 PHE B 263 TYR 0.012 0.002 TYR B 169 ARG 0.005 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04989 ( 250) hydrogen bonds : angle 3.65914 ( 633) metal coordination : bond 0.00729 ( 4) metal coordination : angle 1.19417 ( 3) covalent geometry : bond 0.00409 ( 6569) covalent geometry : angle 0.65369 ( 9430) *********************** 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 66 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.485 Fit side-chains REVERT: B 44 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7588 (mp) REVERT: B 47 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7032 (mtp-110) REVERT: B 132 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6522 (tmm160) REVERT: B 180 THR cc_start: 0.7523 (p) cc_final: 0.7066 (t) REVERT: B 307 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.6242 (m-80) REVERT: B 452 TRP cc_start: 0.6715 (OUTLIER) cc_final: 0.5424 (t-100) REVERT: B 491 ARG cc_start: 0.6638 (ttm170) cc_final: 0.6379 (mtt180) REVERT: B 557 ASN cc_start: 0.8223 (m-40) cc_final: 0.7993 (m110) REVERT: B 596 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6445 (m-10) outliers start: 18 outliers final: 6 residues processed: 57 average time/residue: 1.2454 time to fit residues: 74.5335 Evaluate side-chains 56 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 33 ARG 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 307 PHE Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 494 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 47 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4308 r_free = 0.4308 target = 0.187037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153083 restraints weight = 8165.279| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.49 r_work: 0.3765 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6573 Z= 0.125 Angle : 0.580 7.314 9433 Z= 0.292 Chirality : 0.034 0.161 1149 Planarity : 0.004 0.047 740 Dihedral : 23.113 178.883 2432 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.96 % Allowed : 31.66 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.42), residues: 417 helix: 1.08 (0.35), residues: 224 sheet: 1.19 (0.81), residues: 38 loop : -2.28 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 452 HIS 0.002 0.001 HIS B 136 PHE 0.025 0.002 PHE B 263 TYR 0.010 0.001 TYR B 169 ARG 0.006 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 250) hydrogen bonds : angle 3.45130 ( 633) metal coordination : bond 0.00330 ( 4) metal coordination : angle 0.66976 ( 3) covalent geometry : bond 0.00259 ( 6569) covalent geometry : angle 0.58022 ( 9430) ********************** 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 56 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.537 Fit side-chains REVERT: B 33 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.5700 (ptm-80) REVERT: B 44 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7505 (mp) REVERT: B 47 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7139 (mtp180) REVERT: B 132 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6280 (tmm160) REVERT: B 180 THR cc_start: 0.7229 (p) cc_final: 0.6794 (t) REVERT: B 207 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7289 (ptp-110) REVERT: B 307 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.6058 (m-80) REVERT: B 452 TRP cc_start: 0.6694 (OUTLIER) cc_final: 0.5382 (t-100) REVERT: B 491 ARG cc_start: 0.6480 (ttm170) cc_final: 0.6246 (mtt180) REVERT: B 503 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7568 (mt) outliers start: 15 outliers final: 6 residues processed: 51 average time/residue: 1.3274 time to fit residues: 70.9967 Evaluate side-chains 52 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 16 THR 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 47 ARG Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 567 THR 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 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.185434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.147978 restraints weight = 8201.521| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.28 r_work: 0.3766 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6573 Z= 0.146 Angle : 0.598 7.468 9433 Z= 0.299 Chirality : 0.034 0.150 1149 Planarity : 0.004 0.049 740 Dihedral : 23.101 176.901 2432 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.56 % Favored : 95.20 % Rotamer: Outliers : 3.69 % Allowed : 31.66 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.42), residues: 417 helix: 1.19 (0.36), residues: 222 sheet: 1.26 (0.82), residues: 38 loop : -2.28 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 452 HIS 0.003 0.001 HIS B 497 PHE 0.026 0.002 PHE B 263 TYR 0.010 0.001 TYR B 169 ARG 0.006 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 250) hydrogen bonds : angle 3.46917 ( 633) metal coordination : bond 0.00489 ( 4) metal coordination : angle 0.79637 ( 3) covalent geometry : bond 0.00302 ( 6569) covalent geometry : angle 0.59753 ( 9430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4655.24 seconds wall clock time: 80 minutes 55.19 seconds (4855.19 seconds total)