Starting phenix.real_space_refine on Sat May 10 21:09:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rlb_19337/05_2025/8rlb_19337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rlb_19337/05_2025/8rlb_19337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rlb_19337/05_2025/8rlb_19337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rlb_19337/05_2025/8rlb_19337.map" model { file = "/net/cci-nas-00/data/ceres_data/8rlb_19337/05_2025/8rlb_19337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rlb_19337/05_2025/8rlb_19337.cif" } resolution = 2.99 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= 0.018 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 2231 2.51 5 N 614 2.21 5 O 696 1.98 5 H 3337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 6894 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3450 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1699 Classifications: {'peptide': 114} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1745 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 4.69, per 1000 atoms: 0.68 Number of scatterers: 6894 At special positions: 0 Unit cell: (63.08, 84.66, 78.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 696 8.00 N 614 7.00 C 2231 6.00 H 3337 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS K 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 585.0 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 832 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 6 sheets defined 6.9% alpha, 43.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 56 through 65 removed outlier: 3.816A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'D' and resid 83 through 88 removed outlier: 4.464A pdb=" N ALA D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 22 removed outlier: 5.496A pdb=" N ASN B 149 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS B 166 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 161 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.145A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'K' and resid 30 through 31 removed outlier: 3.881A pdb=" N SER K 30 " --> pdb=" O TYR K 101 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR K 101 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG K 33 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 30 through 31 removed outlier: 3.881A pdb=" N SER K 30 " --> pdb=" O TYR K 101 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR K 101 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR K 98 " --> pdb=" O TYR K 114 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR K 114 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR K 100 " --> pdb=" O ASP K 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP K 112 " --> pdb=" O THR K 100 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3335 1.03 - 1.23: 3 1.23 - 1.42: 1583 1.42 - 1.62: 2025 1.62 - 1.81: 26 Bond restraints: 6972 Sorted by residual: bond pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.17e-02 7.31e+03 7.70e+00 bond pdb=" N LEU B 207 " pdb=" CA LEU B 207 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.19e-02 7.06e+03 6.81e+00 bond pdb=" N THR B 203 " pdb=" H THR B 203 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" N SER B 205 " pdb=" H SER B 205 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.43e+00 bond pdb=" N VAL B 206 " pdb=" H VAL B 206 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.43e+00 ... (remaining 6967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 11489 0.90 - 1.80: 936 1.80 - 2.70: 45 2.70 - 3.60: 23 3.60 - 4.50: 10 Bond angle restraints: 12503 Sorted by residual: angle pdb=" CA THR B 203 " pdb=" C THR B 203 " pdb=" O THR B 203 " ideal model delta sigma weight residual 120.70 116.93 3.77 1.08e+00 8.57e-01 1.22e+01 angle pdb=" CA VAL B 206 " pdb=" C VAL B 206 " pdb=" O VAL B 206 " ideal model delta sigma weight residual 120.39 117.29 3.10 1.05e+00 9.07e-01 8.73e+00 angle pdb=" CA GLN B 204 " pdb=" C GLN B 204 " pdb=" O GLN B 204 " ideal model delta sigma weight residual 120.30 117.21 3.09 1.07e+00 8.73e-01 8.34e+00 angle pdb=" CA LEU B 207 " pdb=" C LEU B 207 " pdb=" O LEU B 207 " ideal model delta sigma weight residual 121.16 118.05 3.11 1.13e+00 7.83e-01 7.55e+00 angle pdb=" CA SER B 205 " pdb=" C SER B 205 " pdb=" O SER B 205 " ideal model delta sigma weight residual 120.36 117.60 2.76 1.08e+00 8.57e-01 6.53e+00 ... (remaining 12498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 2994 15.58 - 31.16: 228 31.16 - 46.74: 68 46.74 - 62.31: 31 62.31 - 77.89: 4 Dihedral angle restraints: 3325 sinusoidal: 1759 harmonic: 1566 Sorted by residual: dihedral pdb=" CB CYS D 11 " pdb=" SG CYS D 11 " pdb=" SG CYS K 11 " pdb=" CB CYS K 11 " ideal model delta sinusoidal sigma weight residual -86.00 -136.55 50.55 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CB MET B 218 " pdb=" CG MET B 218 " pdb=" SD MET B 218 " pdb=" CE MET B 218 " ideal model delta sinusoidal sigma weight residual -60.00 -105.65 45.65 3 1.50e+01 4.44e-03 8.21e+00 dihedral pdb=" CB GLU D 46 " pdb=" CG GLU D 46 " pdb=" CD GLU D 46 " pdb=" OE1 GLU D 46 " ideal model delta sinusoidal sigma weight residual 0.00 76.55 -76.55 1 3.00e+01 1.11e-03 8.19e+00 ... (remaining 3322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 374 0.038 - 0.077: 97 0.077 - 0.115: 48 0.115 - 0.153: 8 0.153 - 0.192: 2 Chirality restraints: 529 Sorted by residual: chirality pdb=" CA VAL B 206 " pdb=" N VAL B 206 " pdb=" C VAL B 206 " pdb=" CB VAL B 206 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA ILE B 152 " pdb=" N ILE B 152 " pdb=" C ILE B 152 " pdb=" CB ILE B 152 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA GLN B 204 " pdb=" N GLN B 204 " pdb=" C GLN B 204 " pdb=" CB GLN B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 526 not shown) Planarity restraints: 1093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 204 " 0.076 2.00e-02 2.50e+03 8.00e-02 9.61e+01 pdb=" CD GLN B 204 " -0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN B 204 " -0.072 2.00e-02 2.50e+03 pdb=" NE2 GLN B 204 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 204 " -0.116 2.00e-02 2.50e+03 pdb="HE22 GLN B 204 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 210 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO B 211 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 181 " 0.003 2.00e-02 2.50e+03 8.42e-03 1.59e+00 pdb=" CG HIS B 181 " -0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS B 181 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS B 181 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 181 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 181 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS B 181 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS B 181 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS B 181 " -0.002 2.00e-02 2.50e+03 ... (remaining 1090 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 597 2.22 - 2.82: 14619 2.82 - 3.41: 17841 3.41 - 4.01: 24749 4.01 - 4.60: 36891 Nonbonded interactions: 94697 Sorted by model distance: nonbonded pdb=" O CYS B 70 " pdb=" HZ1 LYS B 85 " model vdw 1.626 2.450 nonbonded pdb=" HZ2 LYS B 166 " pdb=" OD1 ASP B 180 " model vdw 1.649 2.450 nonbonded pdb=" O PRO B 56 " pdb=" HG1 THR B 59 " model vdw 1.733 2.450 nonbonded pdb=" O GLU B 213 " pdb=" HE2 HIS B 217 " model vdw 1.734 2.450 nonbonded pdb=" OE2 GLU B 115 " pdb="HH12 ARG B 122 " model vdw 1.756 2.450 ... (remaining 94692 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=0.00 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: 6.130 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.600 Find NCS groups from input model: 0.040 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 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 : 0.002 0.032 3637 Z= 0.135 Angle : 0.485 4.500 4934 Z= 0.277 Chirality : 0.045 0.192 529 Planarity : 0.003 0.035 650 Dihedral : 12.441 77.892 1297 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.25 (0.40), residues: 457 helix: -0.71 (1.32), residues: 19 sheet: 0.47 (0.36), residues: 207 loop : 0.08 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 101 HIS 0.015 0.002 HIS B 181 PHE 0.011 0.001 PHE D 67 TYR 0.011 0.001 TYR K 37 ARG 0.002 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.10021 ( 156) hydrogen bonds : angle 6.80497 ( 396) SS BOND : bond 0.00101 ( 2) SS BOND : angle 1.08925 ( 4) covalent geometry : bond 0.00228 ( 3635) covalent geometry : angle 0.48447 ( 4930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 PHE cc_start: 0.6260 (m-10) cc_final: 0.5750 (m-10) REVERT: D 82 MET cc_start: 0.7550 (mmm) cc_final: 0.7293 (mmt) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 1.9001 time to fit residues: 204.5998 Evaluate side-chains 93 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 40 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.146020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.134064 restraints weight = 17141.019| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.90 r_work: 0.3839 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3637 Z= 0.172 Angle : 0.573 5.809 4934 Z= 0.302 Chirality : 0.047 0.170 529 Planarity : 0.004 0.041 650 Dihedral : 4.101 13.707 505 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 12.97 % Favored : 85.14 % 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: 0.26 (0.41), residues: 457 helix: -0.01 (1.54), residues: 13 sheet: 0.36 (0.36), residues: 211 loop : 0.14 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 36 HIS 0.006 0.001 HIS B 181 PHE 0.012 0.002 PHE B 84 TYR 0.012 0.001 TYR B 143 ARG 0.005 0.001 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 156) hydrogen bonds : angle 6.13462 ( 396) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.36674 ( 4) covalent geometry : bond 0.00396 ( 3635) covalent geometry : angle 0.57184 ( 4930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 111 average time/residue: 1.8689 time to fit residues: 215.0556 Evaluate side-chains 100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain D residue 58 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.125906 restraints weight = 17102.665| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.84 r_work: 0.3724 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3637 Z= 0.191 Angle : 0.569 5.305 4934 Z= 0.305 Chirality : 0.047 0.164 529 Planarity : 0.004 0.048 650 Dihedral : 4.505 15.592 505 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.89 % Allowed : 16.76 % Favored : 81.35 % 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: -0.08 (0.40), residues: 457 helix: -0.24 (1.58), residues: 13 sheet: 0.15 (0.36), residues: 211 loop : -0.10 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 115 HIS 0.005 0.001 HIS B 181 PHE 0.019 0.002 PHE K 67 TYR 0.016 0.002 TYR B 143 ARG 0.003 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 156) hydrogen bonds : angle 6.29923 ( 396) SS BOND : bond 0.00301 ( 2) SS BOND : angle 1.31368 ( 4) covalent geometry : bond 0.00440 ( 3635) covalent geometry : angle 0.56776 ( 4930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.7051 (mtm-85) REVERT: D 17 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8400 (m) REVERT: K 34 MET cc_start: 0.7680 (mmt) cc_final: 0.7362 (mmm) outliers start: 7 outliers final: 3 residues processed: 105 average time/residue: 1.8535 time to fit residues: 201.8250 Evaluate side-chains 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain K residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 6 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN B 183 GLN K 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.136494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.124121 restraints weight = 17319.529| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.85 r_work: 0.3692 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3637 Z= 0.170 Angle : 0.553 5.941 4934 Z= 0.294 Chirality : 0.046 0.156 529 Planarity : 0.004 0.046 650 Dihedral : 4.472 16.028 505 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.08 % Allowed : 20.27 % Favored : 78.65 % 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: -0.24 (0.40), residues: 457 helix: -0.76 (1.53), residues: 13 sheet: 0.08 (0.36), residues: 211 loop : -0.23 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 115 HIS 0.005 0.001 HIS B 181 PHE 0.013 0.002 PHE K 67 TYR 0.016 0.001 TYR B 143 ARG 0.003 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 156) hydrogen bonds : angle 6.17753 ( 396) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.74394 ( 4) covalent geometry : bond 0.00393 ( 3635) covalent geometry : angle 0.55265 ( 4930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLN cc_start: 0.7711 (mt0) cc_final: 0.7355 (mp10) REVERT: D 17 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8458 (m) REVERT: K 34 MET cc_start: 0.7646 (mmt) cc_final: 0.7348 (mmm) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 1.8483 time to fit residues: 184.0835 Evaluate side-chains 97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain K residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN K 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.133048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.120798 restraints weight = 17148.233| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.76 r_work: 0.3649 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3637 Z= 0.215 Angle : 0.584 6.055 4934 Z= 0.315 Chirality : 0.047 0.159 529 Planarity : 0.005 0.054 650 Dihedral : 4.739 16.175 505 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.89 % Allowed : 20.27 % Favored : 77.84 % 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: -0.52 (0.40), residues: 457 helix: -1.35 (1.46), residues: 13 sheet: -0.15 (0.36), residues: 213 loop : -0.34 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 115 HIS 0.002 0.001 HIS B 181 PHE 0.013 0.002 PHE K 67 TYR 0.018 0.002 TYR B 92 ARG 0.004 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 156) hydrogen bonds : angle 6.41359 ( 396) SS BOND : bond 0.00384 ( 2) SS BOND : angle 1.04944 ( 4) covalent geometry : bond 0.00498 ( 3635) covalent geometry : angle 0.58327 ( 4930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8567 (m) REVERT: K 34 MET cc_start: 0.7918 (mmt) cc_final: 0.7605 (mmm) outliers start: 7 outliers final: 2 residues processed: 102 average time/residue: 1.8663 time to fit residues: 197.5709 Evaluate side-chains 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain K residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 43 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS B 159 ASN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.134811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122144 restraints weight = 17236.820| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.85 r_work: 0.3662 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3637 Z= 0.157 Angle : 0.556 5.569 4934 Z= 0.296 Chirality : 0.046 0.154 529 Planarity : 0.005 0.048 650 Dihedral : 4.570 16.253 505 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.89 % Allowed : 20.81 % Favored : 77.30 % 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: -0.53 (0.40), residues: 457 helix: -1.47 (1.46), residues: 13 sheet: -0.12 (0.37), residues: 212 loop : -0.38 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 115 HIS 0.002 0.000 HIS B 181 PHE 0.008 0.001 PHE K 67 TYR 0.012 0.001 TYR B 92 ARG 0.009 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 156) hydrogen bonds : angle 6.35662 ( 396) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.59767 ( 4) covalent geometry : bond 0.00362 ( 3635) covalent geometry : angle 0.55624 ( 4930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.7416 (mtp-110) cc_final: 0.7107 (mtm-85) REVERT: D 17 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8535 (m) REVERT: K 34 MET cc_start: 0.7654 (mmt) cc_final: 0.7379 (mmm) outliers start: 7 outliers final: 2 residues processed: 100 average time/residue: 2.0291 time to fit residues: 209.9214 Evaluate side-chains 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain K residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.121223 restraints weight = 16960.704| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.83 r_work: 0.3646 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3637 Z= 0.178 Angle : 0.570 6.628 4934 Z= 0.302 Chirality : 0.046 0.154 529 Planarity : 0.005 0.049 650 Dihedral : 4.644 15.913 505 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.62 % Allowed : 21.35 % Favored : 77.03 % 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: -0.67 (0.39), residues: 457 helix: -1.83 (1.32), residues: 13 sheet: -0.21 (0.36), residues: 209 loop : -0.47 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 101 HIS 0.002 0.001 HIS B 181 PHE 0.010 0.002 PHE B 46 TYR 0.016 0.002 TYR B 92 ARG 0.010 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 156) hydrogen bonds : angle 6.39297 ( 396) SS BOND : bond 0.00351 ( 2) SS BOND : angle 0.89140 ( 4) covalent geometry : bond 0.00412 ( 3635) covalent geometry : angle 0.56974 ( 4930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8579 (m) REVERT: K 34 MET cc_start: 0.7658 (mmt) cc_final: 0.7389 (mmm) outliers start: 6 outliers final: 3 residues processed: 102 average time/residue: 1.8891 time to fit residues: 199.9801 Evaluate side-chains 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 33 optimal weight: 0.0030 chunk 41 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS B 159 ASN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.134784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122091 restraints weight = 17189.987| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.87 r_work: 0.3671 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3637 Z= 0.138 Angle : 0.566 6.858 4934 Z= 0.296 Chirality : 0.046 0.154 529 Planarity : 0.005 0.044 650 Dihedral : 4.505 15.726 505 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.81 % Allowed : 22.97 % Favored : 76.22 % 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: -0.57 (0.40), residues: 457 helix: -1.63 (1.42), residues: 13 sheet: -0.42 (0.35), residues: 220 loop : -0.07 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 101 HIS 0.002 0.001 HIS B 181 PHE 0.008 0.001 PHE B 165 TYR 0.013 0.001 TYR B 143 ARG 0.010 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.02923 ( 156) hydrogen bonds : angle 6.33938 ( 396) SS BOND : bond 0.00247 ( 2) SS BOND : angle 0.50019 ( 4) covalent geometry : bond 0.00322 ( 3635) covalent geometry : angle 0.56625 ( 4930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.7436 (mtp-110) cc_final: 0.7119 (mtm-85) REVERT: D 17 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8572 (m) REVERT: K 34 MET cc_start: 0.7608 (mmt) cc_final: 0.7340 (mmm) outliers start: 3 outliers final: 3 residues processed: 98 average time/residue: 1.8550 time to fit residues: 188.8768 Evaluate side-chains 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 33 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 0 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.134606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.122117 restraints weight = 17287.223| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.82 r_work: 0.3672 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3637 Z= 0.141 Angle : 0.584 9.446 4934 Z= 0.303 Chirality : 0.046 0.154 529 Planarity : 0.005 0.046 650 Dihedral : 4.514 15.473 505 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.08 % Allowed : 22.70 % Favored : 76.22 % 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: -0.59 (0.40), residues: 457 helix: -1.47 (1.49), residues: 13 sheet: -0.41 (0.35), residues: 219 loop : -0.12 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 101 HIS 0.003 0.001 HIS B 181 PHE 0.008 0.001 PHE D 27 TYR 0.013 0.001 TYR B 143 ARG 0.010 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 156) hydrogen bonds : angle 6.32454 ( 396) SS BOND : bond 0.00326 ( 2) SS BOND : angle 0.62190 ( 4) covalent geometry : bond 0.00336 ( 3635) covalent geometry : angle 0.58395 ( 4930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.7571 (mtp-110) cc_final: 0.7222 (mtm-85) REVERT: K 34 MET cc_start: 0.7821 (mmt) cc_final: 0.7531 (mmm) outliers start: 4 outliers final: 3 residues processed: 98 average time/residue: 1.8622 time to fit residues: 189.9713 Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 18 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS B 159 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.120005 restraints weight = 17472.413| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.84 r_work: 0.3645 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3637 Z= 0.186 Angle : 0.618 8.768 4934 Z= 0.321 Chirality : 0.047 0.154 529 Planarity : 0.005 0.047 650 Dihedral : 4.698 15.363 505 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.81 % Allowed : 24.32 % Favored : 74.86 % 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: -0.60 (0.40), residues: 457 helix: -1.95 (1.32), residues: 13 sheet: -0.25 (0.36), residues: 210 loop : -0.30 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 101 HIS 0.003 0.001 HIS B 181 PHE 0.010 0.002 PHE B 84 TYR 0.017 0.002 TYR B 92 ARG 0.010 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 156) hydrogen bonds : angle 6.34777 ( 396) SS BOND : bond 0.00390 ( 2) SS BOND : angle 0.91863 ( 4) covalent geometry : bond 0.00437 ( 3635) covalent geometry : angle 0.61729 ( 4930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLN cc_start: 0.7864 (mt0) cc_final: 0.7613 (mp10) REVERT: K 34 MET cc_start: 0.7826 (mmt) cc_final: 0.7556 (mmm) outliers start: 3 outliers final: 4 residues processed: 100 average time/residue: 1.8391 time to fit residues: 190.9535 Evaluate side-chains 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 0.0010 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.120026 restraints weight = 17270.561| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.79 r_work: 0.3640 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3637 Z= 0.183 Angle : 0.627 9.851 4934 Z= 0.324 Chirality : 0.046 0.154 529 Planarity : 0.005 0.049 650 Dihedral : 4.722 15.386 505 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.81 % Allowed : 25.14 % Favored : 74.05 % 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: -0.58 (0.40), residues: 457 helix: -1.79 (1.40), residues: 13 sheet: -0.26 (0.36), residues: 210 loop : -0.28 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 101 HIS 0.003 0.001 HIS B 181 PHE 0.009 0.002 PHE D 27 TYR 0.017 0.002 TYR B 143 ARG 0.010 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 156) hydrogen bonds : angle 6.40589 ( 396) SS BOND : bond 0.00382 ( 2) SS BOND : angle 0.87241 ( 4) covalent geometry : bond 0.00431 ( 3635) covalent geometry : angle 0.62659 ( 4930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6019.50 seconds wall clock time: 104 minutes 3.21 seconds (6243.21 seconds total)