Starting phenix.real_space_refine on Wed Sep 17 06:25:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zq9_60379/09_2025/8zq9_60379_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zq9_60379/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zq9_60379/09_2025/8zq9_60379_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zq9_60379/09_2025/8zq9_60379_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zq9_60379/09_2025/8zq9_60379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zq9_60379/09_2025/8zq9_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-2.0-5805/lib/python3.9/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: 1.86, per 1000 atoms: 0.30 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: 0.57 Conformation dependent library (CDL) restraints added in 326.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.89 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: 1.20 Time building geometry restraints manager: 0.76 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: 2.050 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.580 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: 0.010 Load rotamer database and sin/cos tables:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.110 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00745 ( 6569) covalent geometry : angle 1.12953 ( 9430) hydrogen bonds : bond 0.17627 ( 250) hydrogen bonds : angle 7.26381 ( 633) metal coordination : bond 0.00414 ( 4) metal coordination : angle 1.02258 ( 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 : 0.173 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: 0.6506 time to fit residues: 36.7670 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 : 0.180 ------------------------------------------------------------------------------- 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: 10.0000 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... 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 = 0.4279 r_free = 0.4279 target = 0.184065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145624 restraints weight = 8099.281| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.34 r_work: 0.3734 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6573 Z= 0.213 Angle : 0.707 10.276 9433 Z= 0.359 Chirality : 0.040 0.203 1149 Planarity : 0.005 0.069 740 Dihedral : 23.791 171.395 2438 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.49 % Allowed : 24.80 % Favored : 70.71 % 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 aren not related in a simple way. whole: -1.27 (0.40), residues: 417 helix: 0.32 (0.35), residues: 224 sheet: -0.16 (0.75), residues: 39 loop : -2.84 (0.44), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 207 TYR 0.010 0.002 TYR B 70 PHE 0.029 0.002 PHE B 263 TRP 0.009 0.002 TRP B 452 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 6569) covalent geometry : angle 0.70625 ( 9430) hydrogen bonds : bond 0.04831 ( 250) hydrogen bonds : angle 4.22889 ( 633) metal coordination : bond 0.00726 ( 4) metal coordination : angle 1.39538 ( 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 61 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 35 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7294 (pptt) REVERT: B 47 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.6988 (ttp-110) REVERT: B 162 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: B 314 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.5903 (tmt) REVERT: B 503 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7410 (mt) REVERT: B 596 PHE cc_start: 0.6487 (m-10) cc_final: 0.6237 (m-10) outliers start: 17 outliers final: 8 residues processed: 56 average time/residue: 0.6470 time to fit residues: 37.9222 Evaluate side-chains 53 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 314 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 572 VAL 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: 2.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 B 496 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.180937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.146501 restraints weight = 8056.291| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.47 r_work: 0.3682 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6573 Z= 0.225 Angle : 0.692 9.639 9433 Z= 0.351 Chirality : 0.040 0.214 1149 Planarity : 0.005 0.065 740 Dihedral : 23.639 174.511 2432 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.80 % Allowed : 24.54 % Favored : 69.66 % 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 aren not related in a simple way. whole: -1.07 (0.41), residues: 417 helix: 0.40 (0.35), residues: 224 sheet: 0.16 (0.76), residues: 39 loop : -2.66 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 207 TYR 0.012 0.002 TYR B 169 PHE 0.031 0.003 PHE B 263 TRP 0.006 0.002 TRP B 452 HIS 0.004 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 6569) covalent geometry : angle 0.69128 ( 9430) hydrogen bonds : bond 0.05487 ( 250) hydrogen bonds : angle 4.07363 ( 633) metal coordination : bond 0.01477 ( 4) metal coordination : angle 1.51257 ( 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 67 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.187 Fit side-chains REVERT: B 36 MET cc_start: 0.8596 (mpp) cc_final: 0.8368 (mtt) REVERT: B 44 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7703 (mp) REVERT: B 47 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7079 (mtp-110) REVERT: B 162 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: B 180 THR cc_start: 0.7258 (p) cc_final: 0.6892 (t) REVERT: B 314 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6539 (tmm) outliers start: 22 outliers final: 9 residues processed: 59 average time/residue: 0.6278 time to fit residues: 38.7987 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 : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 44 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 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 567 THR 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: 1.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.182846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.144575 restraints weight = 8133.948| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.30 r_work: 0.3722 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6573 Z= 0.174 Angle : 0.627 9.810 9433 Z= 0.314 Chirality : 0.037 0.206 1149 Planarity : 0.004 0.058 740 Dihedral : 23.424 175.852 2432 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.28 % Allowed : 27.18 % Favored : 67.55 % 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 aren not related in a simple way. whole: -0.67 (0.41), residues: 417 helix: 0.60 (0.35), residues: 224 sheet: 1.02 (0.78), residues: 37 loop : -2.43 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 207 TYR 0.009 0.001 TYR B 169 PHE 0.027 0.002 PHE B 263 TRP 0.006 0.001 TRP B 484 HIS 0.003 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6569) covalent geometry : angle 0.62642 ( 9430) hydrogen bonds : bond 0.04641 ( 250) hydrogen bonds : angle 3.77879 ( 633) metal coordination : bond 0.00801 ( 4) metal coordination : angle 1.29553 ( 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 64 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.178 Fit side-chains REVERT: B 44 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7496 (mp) REVERT: B 47 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6972 (ttp-110) REVERT: B 132 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6410 (ttm170) REVERT: B 162 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: B 314 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6423 (tmm) REVERT: B 452 TRP cc_start: 0.6510 (OUTLIER) cc_final: 0.5333 (t-100) outliers start: 20 outliers final: 8 residues processed: 57 average time/residue: 0.6841 time to fit residues: 40.7165 Evaluate side-chains 54 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR 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 314 MET 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 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: 3.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4249 r_free = 0.4249 target = 0.181385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.142738 restraints weight = 8222.940| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.33 r_work: 0.3701 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3148 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= 0.203 Angle : 0.660 10.038 9433 Z= 0.332 Chirality : 0.039 0.212 1149 Planarity : 0.004 0.059 740 Dihedral : 23.387 174.382 2432 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 6.60 % Allowed : 25.59 % Favored : 67.81 % 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 aren not related in a simple way. whole: -0.69 (0.41), residues: 417 helix: 0.55 (0.35), residues: 224 sheet: 1.19 (0.81), residues: 37 loop : -2.43 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 207 TYR 0.011 0.001 TYR B 169 PHE 0.028 0.002 PHE B 263 TRP 0.008 0.001 TRP B 484 HIS 0.004 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6569) covalent geometry : angle 0.65950 ( 9430) hydrogen bonds : bond 0.05080 ( 250) hydrogen bonds : angle 3.77964 ( 633) metal coordination : bond 0.00777 ( 4) metal coordination : angle 1.59895 ( 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 67 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 0.187 Fit side-chains REVERT: B 36 MET cc_start: 0.8643 (mpp) cc_final: 0.8367 (mtt) REVERT: B 44 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7562 (mp) REVERT: B 47 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7018 (ttp-110) REVERT: B 132 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6472 (ttm170) REVERT: B 162 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: B 168 GLN cc_start: 0.8617 (tp-100) cc_final: 0.7885 (tp-100) REVERT: B 314 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6567 (tmm) REVERT: B 452 TRP cc_start: 0.6534 (OUTLIER) cc_final: 0.5383 (t-100) REVERT: B 557 ASN cc_start: 0.8238 (m-40) cc_final: 0.8002 (m110) outliers start: 25 outliers final: 13 residues processed: 59 average time/residue: 0.6733 time to fit residues: 41.5309 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 : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR 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 258 SER Chi-restraints excluded: chain B residue 261 THR 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 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 567 THR Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 611 GLU 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: 5.9990 chunk 33 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 0.0570 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4300 r_free = 0.4300 target = 0.186231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152104 restraints weight = 8193.460| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.51 r_work: 0.3756 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6573 Z= 0.130 Angle : 0.582 10.162 9433 Z= 0.290 Chirality : 0.035 0.212 1149 Planarity : 0.004 0.054 740 Dihedral : 23.320 178.635 2432 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.28 % Allowed : 28.23 % Favored : 66.49 % 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 aren not related in a simple way. whole: -0.26 (0.42), residues: 417 helix: 0.92 (0.36), residues: 224 sheet: 1.63 (0.80), residues: 37 loop : -2.33 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 283 TYR 0.007 0.001 TYR B 169 PHE 0.023 0.002 PHE B 263 TRP 0.008 0.001 TRP B 484 HIS 0.001 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6569) covalent geometry : angle 0.58182 ( 9430) hydrogen bonds : bond 0.04030 ( 250) hydrogen bonds : angle 3.54986 ( 633) metal coordination : bond 0.00456 ( 4) metal coordination : angle 1.23027 ( 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 69 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.198 Fit side-chains REVERT: B 35 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7295 (pptt) REVERT: B 44 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7556 (mp) REVERT: B 47 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7137 (mtp180) REVERT: B 132 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6280 (tmm160) REVERT: B 162 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: B 203 GLU cc_start: 0.7396 (tt0) cc_final: 0.7168 (tp30) REVERT: B 452 TRP cc_start: 0.6532 (OUTLIER) cc_final: 0.5357 (t-100) REVERT: B 557 ASN cc_start: 0.8134 (m-40) cc_final: 0.7928 (m110) outliers start: 20 outliers final: 9 residues processed: 60 average time/residue: 0.7160 time to fit residues: 44.7268 Evaluate side-chains 55 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 452 TRP Chi-restraints excluded: chain B residue 485 TRP 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 611 GLU 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: 0.9980 chunk 35 optimal weight: 0.0070 chunk 23 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.186217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.152441 restraints weight = 8160.954| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.43 r_work: 0.3760 rms_B_bonded: 2.77 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: 0.7558 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6573 Z= 0.135 Angle : 0.590 9.911 9433 Z= 0.293 Chirality : 0.034 0.205 1149 Planarity : 0.004 0.051 740 Dihedral : 23.229 177.391 2432 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.80 % Allowed : 28.23 % 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 aren not related in a simple way. whole: -0.14 (0.42), residues: 417 helix: 1.10 (0.36), residues: 222 sheet: 1.71 (0.79), residues: 37 loop : -2.39 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 207 TYR 0.008 0.001 TYR B 70 PHE 0.022 0.002 PHE B 263 TRP 0.010 0.001 TRP B 484 HIS 0.003 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6569) covalent geometry : angle 0.58981 ( 9430) hydrogen bonds : bond 0.04144 ( 250) hydrogen bonds : angle 3.48465 ( 633) metal coordination : bond 0.00419 ( 4) metal coordination : angle 1.03840 ( 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 67 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.175 Fit side-chains REVERT: B 35 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7299 (pptt) REVERT: B 44 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7647 (mp) REVERT: B 47 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7122 (mtp180) REVERT: B 123 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6695 (mp0) REVERT: B 132 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6258 (tmm160) REVERT: B 162 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: B 168 GLN cc_start: 0.8455 (tp-100) cc_final: 0.7687 (tp-100) REVERT: B 203 GLU cc_start: 0.7382 (tt0) cc_final: 0.7077 (tp30) REVERT: B 262 VAL cc_start: 0.5664 (OUTLIER) cc_final: 0.5424 (m) REVERT: B 452 TRP cc_start: 0.6638 (OUTLIER) cc_final: 0.5443 (t-100) REVERT: B 557 ASN cc_start: 0.8125 (m-40) cc_final: 0.7889 (m110) REVERT: B 596 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.6380 (m-10) outliers start: 22 outliers final: 8 residues processed: 61 average time/residue: 0.6820 time to fit residues: 43.4205 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 : 0.172 ------------------------------------------------------------------------------- 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 208 PHE 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 567 THR Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 611 GLU 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: 0.5980 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.186748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.152725 restraints weight = 8157.639| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.41 r_work: 0.3765 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6573 Z= 0.135 Angle : 0.583 9.444 9433 Z= 0.291 Chirality : 0.034 0.193 1149 Planarity : 0.004 0.051 740 Dihedral : 23.206 177.646 2432 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.54 % Allowed : 27.97 % Favored : 66.49 % 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 aren not related in a simple way. whole: 0.00 (0.42), residues: 417 helix: 1.16 (0.36), residues: 224 sheet: 1.86 (0.77), residues: 37 loop : -2.30 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 207 TYR 0.009 0.001 TYR B 169 PHE 0.022 0.002 PHE B 263 TRP 0.009 0.001 TRP B 484 HIS 0.001 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6569) covalent geometry : angle 0.58303 ( 9430) hydrogen bonds : bond 0.04054 ( 250) hydrogen bonds : angle 3.44544 ( 633) metal coordination : bond 0.00336 ( 4) metal coordination : angle 0.78727 ( 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 64 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.190 Fit side-chains REVERT: B 35 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7333 (pptt) REVERT: B 44 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 47 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7048 (mtp180) REVERT: B 123 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6691 (mp0) REVERT: B 132 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6164 (tmm160) REVERT: B 162 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: B 262 VAL cc_start: 0.5679 (OUTLIER) cc_final: 0.5443 (m) REVERT: B 314 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6352 (tmt) REVERT: B 452 TRP cc_start: 0.6684 (OUTLIER) cc_final: 0.5461 (t-100) REVERT: B 557 ASN cc_start: 0.8116 (m-40) cc_final: 0.7889 (m110) outliers start: 21 outliers final: 12 residues processed: 58 average time/residue: 0.6478 time to fit residues: 39.2973 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 : 0.178 ------------------------------------------------------------------------------- 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 162 GLU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 314 MET 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 625 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.186726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.153038 restraints weight = 8191.217| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.48 r_work: 0.3764 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3461 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= 0.134 Angle : 0.585 8.697 9433 Z= 0.293 Chirality : 0.034 0.179 1149 Planarity : 0.004 0.051 740 Dihedral : 23.127 177.834 2432 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.04 % Favored : 94.72 % Rotamer: Outliers : 5.28 % Allowed : 28.76 % 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 aren not related in a simple way. whole: 0.09 (0.42), residues: 417 helix: 1.23 (0.36), residues: 224 sheet: 1.86 (0.75), residues: 37 loop : -2.26 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 207 TYR 0.009 0.001 TYR B 169 PHE 0.023 0.002 PHE B 235 TRP 0.011 0.001 TRP B 484 HIS 0.002 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6569) covalent geometry : angle 0.58524 ( 9430) hydrogen bonds : bond 0.04059 ( 250) hydrogen bonds : angle 3.47123 ( 633) metal coordination : bond 0.00335 ( 4) metal coordination : angle 0.78909 ( 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 63 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.109 Fit side-chains REVERT: B 33 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.5662 (ptm-80) REVERT: B 35 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7257 (pptt) REVERT: B 44 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7650 (mp) REVERT: B 47 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7050 (mtp180) REVERT: B 123 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6666 (mp0) REVERT: B 132 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6287 (tmm160) REVERT: B 162 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: B 262 VAL cc_start: 0.5326 (OUTLIER) cc_final: 0.5100 (m) REVERT: B 452 TRP cc_start: 0.6706 (OUTLIER) cc_final: 0.5492 (t-100) REVERT: B 557 ASN cc_start: 0.8102 (m-40) cc_final: 0.7882 (m110) outliers start: 20 outliers final: 11 residues processed: 56 average time/residue: 0.5879 time to fit residues: 34.3867 Evaluate side-chains 58 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 162 GLU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 GLU 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 625 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.184692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.147065 restraints weight = 8185.826| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.27 r_work: 0.3752 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6573 Z= 0.158 Angle : 0.611 7.171 9433 Z= 0.306 Chirality : 0.035 0.179 1149 Planarity : 0.004 0.052 740 Dihedral : 23.114 176.311 2432 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.28 % Allowed : 29.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.42), residues: 417 helix: 1.13 (0.36), residues: 224 sheet: 1.62 (0.77), residues: 38 loop : -2.31 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 207 TYR 0.014 0.001 TYR B 169 PHE 0.028 0.002 PHE B 263 TRP 0.013 0.001 TRP B 484 HIS 0.003 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6569) covalent geometry : angle 0.61059 ( 9430) hydrogen bonds : bond 0.04441 ( 250) hydrogen bonds : angle 3.51089 ( 633) metal coordination : bond 0.00637 ( 4) metal coordination : angle 0.85208 ( 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 63 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.197 Fit side-chains REVERT: B 35 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7236 (pptt) REVERT: B 44 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7614 (mp) REVERT: B 47 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6965 (mtp-110) REVERT: B 123 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6692 (mp0) REVERT: B 132 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6398 (tmm160) REVERT: B 162 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: B 262 VAL cc_start: 0.5245 (OUTLIER) cc_final: 0.5031 (m) REVERT: B 452 TRP cc_start: 0.6739 (OUTLIER) cc_final: 0.5508 (t-100) REVERT: B 557 ASN cc_start: 0.8154 (m-40) cc_final: 0.7929 (m110) outliers start: 20 outliers final: 10 residues processed: 56 average time/residue: 0.5388 time to fit residues: 31.7436 Evaluate side-chains 58 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 44 LEU Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 73 SER 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 241 THR Chi-restraints excluded: chain B residue 262 VAL 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 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: 3.9990 chunk 30 optimal weight: 0.0050 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.185509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147996 restraints weight = 8135.429| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.28 r_work: 0.3766 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3587 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= 0.143 Angle : 0.599 7.230 9433 Z= 0.302 Chirality : 0.035 0.149 1149 Planarity : 0.004 0.050 740 Dihedral : 23.114 177.300 2432 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.49 % Allowed : 30.08 % Favored : 65.44 % 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 aren not related in a simple way. whole: 0.03 (0.43), residues: 417 helix: 1.19 (0.36), residues: 224 sheet: 1.70 (0.77), residues: 38 loop : -2.28 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 207 TYR 0.011 0.001 TYR B 169 PHE 0.026 0.002 PHE B 263 TRP 0.016 0.001 TRP B 484 HIS 0.002 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6569) covalent geometry : angle 0.59894 ( 9430) hydrogen bonds : bond 0.04253 ( 250) hydrogen bonds : angle 3.50783 ( 633) metal coordination : bond 0.00492 ( 4) metal coordination : angle 0.93983 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.14 seconds wall clock time: 41 minutes 46.65 seconds (2506.65 seconds total)