Starting phenix.real_space_refine on Wed Mar 12 00:05:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rlb_19337/03_2025/8rlb_19337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rlb_19337/03_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_19337/03_2025/8rlb_19337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rlb_19337/03_2025/8rlb_19337.map" model { file = "/net/cci-nas-00/data/ceres_data/8rlb_19337/03_2025/8rlb_19337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rlb_19337/03_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-5624/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: 4.18, per 1000 atoms: 0.61 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: 1.76 Conformation dependent library (CDL) restraints added in 628.0 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: 0.60 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: 2.24 Time building geometry restraints manager: 2.14 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: 3.960 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: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.200 Find NCS groups from input model: 0.050 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:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- 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 3635 Z= 0.157 Angle : 0.484 4.500 4930 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 *********************** 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 : 0.541 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: 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: 1.9682 time to fit residues: 212.0766 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 : 0.541 ------------------------------------------------------------------------------- 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: 0.5980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.147108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.135227 restraints weight = 17164.250| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.89 r_work: 0.3851 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3635 Z= 0.234 Angle : 0.560 5.348 4930 Z= 0.296 Chirality : 0.047 0.159 529 Planarity : 0.004 0.040 650 Dihedral : 4.035 13.375 505 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: 0.19 (0.40), residues: 457 helix: -0.10 (1.47), residues: 13 sheet: 0.35 (0.36), residues: 206 loop : 0.05 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 36 HIS 0.009 0.001 HIS B 181 PHE 0.013 0.002 PHE K 67 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.001 ARG D 71 *********************** 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 110 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.504 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 outliers start: 7 outliers final: 2 residues processed: 108 average time/residue: 1.9468 time to fit residues: 217.9351 Evaluate side-chains 97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.138494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.126409 restraints weight = 17067.918| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.89 r_work: 0.3725 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3635 Z= 0.262 Angle : 0.558 5.288 4930 Z= 0.301 Chirality : 0.046 0.159 529 Planarity : 0.004 0.046 650 Dihedral : 4.458 15.672 505 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.89 % Allowed : 16.22 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.40), residues: 457 helix: -0.21 (1.55), residues: 13 sheet: 0.17 (0.36), residues: 211 loop : -0.05 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 115 HIS 0.004 0.001 HIS B 25 PHE 0.020 0.002 PHE K 67 TYR 0.015 0.002 TYR B 143 ARG 0.002 0.000 ARG K 71 *********************** 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 : 0.537 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: 0.7322 (mtp-110) cc_final: 0.7027 (mtm-85) REVERT: D 17 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8407 (m) REVERT: K 34 MET cc_start: 0.7715 (mmt) cc_final: 0.7395 (mmm) outliers start: 7 outliers final: 2 residues processed: 105 average time/residue: 1.8556 time to fit residues: 202.3156 Evaluate side-chains 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER 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: 1.9990 chunk 40 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 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** 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 = 0.3937 r_free = 0.3937 target = 0.135857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.123705 restraints weight = 17589.591| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.79 r_work: 0.3690 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3635 Z= 0.290 Angle : 0.566 6.116 4930 Z= 0.304 Chirality : 0.046 0.152 529 Planarity : 0.005 0.048 650 Dihedral : 4.547 16.017 505 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.35 % Allowed : 20.27 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.39), residues: 457 helix: -1.02 (1.52), residues: 13 sheet: 0.05 (0.36), residues: 209 loop : -0.28 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 115 HIS 0.003 0.001 HIS B 181 PHE 0.016 0.002 PHE K 67 TYR 0.013 0.002 TYR B 143 ARG 0.004 0.001 ARG B 96 *********************** 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 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 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: B 69 GLN cc_start: 0.7764 (mt0) cc_final: 0.7403 (mp10) REVERT: D 17 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8460 (m) REVERT: K 34 MET cc_start: 0.7690 (mmt) cc_final: 0.7390 (mmm) outliers start: 5 outliers final: 3 residues processed: 99 average time/residue: 1.9074 time to fit residues: 195.8562 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 : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 33 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 overall best weight: 0.2954 ------------------------------------------------------------------------------- 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 ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.138675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.126685 restraints weight = 17091.390| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.75 r_work: 0.3713 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3635 Z= 0.182 Angle : 0.521 4.734 4930 Z= 0.279 Chirality : 0.045 0.147 529 Planarity : 0.004 0.045 650 Dihedral : 4.306 15.886 505 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.54 % Allowed : 21.35 % Favored : 78.11 % 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: -0.19 (0.40), residues: 457 helix: -0.87 (1.56), residues: 13 sheet: 0.11 (0.37), residues: 206 loop : -0.17 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 115 HIS 0.003 0.001 HIS B 181 PHE 0.008 0.001 PHE K 67 TYR 0.023 0.001 TYR B 143 ARG 0.005 0.000 ARG D 19 *********************** 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 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.600 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: 0.8741 (t) cc_final: 0.8487 (m) REVERT: K 34 MET cc_start: 0.7870 (mmt) cc_final: 0.7590 (mmm) outliers start: 2 outliers final: 2 residues processed: 98 average time/residue: 1.7825 time to fit residues: 181.7399 Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE 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: 0.9980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 43 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.132273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.120122 restraints weight = 17344.004| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.77 r_work: 0.3640 rms_B_bonded: 2.75 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: 0.7509 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3635 Z= 0.332 Angle : 0.593 5.789 4930 Z= 0.321 Chirality : 0.047 0.167 529 Planarity : 0.005 0.051 650 Dihedral : 4.788 16.258 505 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.16 % Allowed : 21.62 % 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: -0.62 (0.39), residues: 457 helix: -1.59 (1.39), residues: 13 sheet: -0.23 (0.36), residues: 213 loop : -0.38 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 115 HIS 0.009 0.001 HIS B 181 PHE 0.015 0.002 PHE K 67 TYR 0.019 0.002 TYR B 92 ARG 0.004 0.001 ARG D 19 *********************** 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 109 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.551 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: 0.7936 (mt0) cc_final: 0.7544 (mp10) REVERT: B 166 LYS cc_start: 0.8356 (mttp) cc_final: 0.7917 (mttp) REVERT: D 17 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8587 (m) REVERT: K 34 MET cc_start: 0.7896 (mmt) cc_final: 0.7597 (mmm) outliers start: 8 outliers final: 4 residues processed: 105 average time/residue: 2.0314 time to fit residues: 221.0001 Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain D residue 7 ASN 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: 1.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 159 ASN ** 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 = 0.3925 r_free = 0.3925 target = 0.135070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122824 restraints weight = 16889.457| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.74 r_work: 0.3664 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3635 Z= 0.238 Angle : 0.559 5.345 4930 Z= 0.298 Chirality : 0.046 0.165 529 Planarity : 0.005 0.049 650 Dihedral : 4.591 16.099 505 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.08 % Allowed : 21.89 % 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: -0.61 (0.39), residues: 457 helix: -1.71 (1.39), residues: 13 sheet: -0.21 (0.36), residues: 209 loop : -0.38 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 115 HIS 0.002 0.001 HIS B 181 PHE 0.008 0.001 PHE K 67 TYR 0.013 0.001 TYR B 92 ARG 0.006 0.001 ARG D 19 *********************** 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 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.495 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: D 17 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8582 (m) REVERT: D 72 ASP cc_start: 0.7585 (t0) cc_final: 0.7371 (t0) REVERT: K 34 MET cc_start: 0.7833 (mmt) cc_final: 0.7557 (mmm) outliers start: 4 outliers final: 1 residues processed: 102 average time/residue: 1.9652 time to fit residues: 207.9874 Evaluate side-chains 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain K residue 35 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.134543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122256 restraints weight = 17093.966| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.74 r_work: 0.3656 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3635 Z= 0.269 Angle : 0.588 6.888 4930 Z= 0.311 Chirality : 0.046 0.155 529 Planarity : 0.005 0.047 650 Dihedral : 4.630 15.923 505 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % 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: -0.67 (0.40), residues: 457 helix: -2.01 (1.30), residues: 13 sheet: -0.25 (0.36), residues: 209 loop : -0.41 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 101 HIS 0.002 0.001 HIS B 181 PHE 0.009 0.002 PHE B 223 TYR 0.016 0.002 TYR B 92 ARG 0.011 0.001 ARG D 19 *********************** 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 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.549 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: K 34 MET cc_start: 0.7829 (mmt) cc_final: 0.7560 (mmm) REVERT: K 117 GLN cc_start: 0.7921 (pm20) cc_final: 0.7619 (pm20) outliers start: 4 outliers final: 4 residues processed: 101 average time/residue: 1.9514 time to fit residues: 205.2715 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 : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 36 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 0 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.134651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122242 restraints weight = 17252.508| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.80 r_work: 0.3674 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3635 Z= 0.216 Angle : 0.577 9.209 4930 Z= 0.301 Chirality : 0.046 0.155 529 Planarity : 0.005 0.047 650 Dihedral : 4.519 17.031 505 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.81 % Allowed : 23.78 % Favored : 75.41 % 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: -0.61 (0.39), residues: 457 helix: -1.76 (1.36), residues: 13 sheet: -0.24 (0.36), residues: 209 loop : -0.35 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 101 HIS 0.001 0.000 HIS B 81 PHE 0.007 0.001 PHE B 223 TYR 0.015 0.001 TYR B 143 ARG 0.012 0.001 ARG D 19 *********************** 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 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.557 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: K 34 MET cc_start: 0.7832 (mmt) cc_final: 0.7546 (mmm) outliers start: 3 outliers final: 4 residues processed: 100 average time/residue: 1.9680 time to fit residues: 204.1316 Evaluate side-chains 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.0000 chunk 18 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.132999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.120040 restraints weight = 17286.699| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.85 r_work: 0.3637 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3635 Z= 0.310 Angle : 0.622 8.728 4930 Z= 0.328 Chirality : 0.047 0.157 529 Planarity : 0.005 0.049 650 Dihedral : 4.748 16.147 505 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.81 % Allowed : 24.05 % Favored : 75.14 % 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: -0.70 (0.40), residues: 457 helix: -1.85 (1.36), residues: 13 sheet: -0.25 (0.36), residues: 209 loop : -0.47 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 101 HIS 0.001 0.000 HIS B 181 PHE 0.013 0.002 PHE B 46 TYR 0.020 0.002 TYR B 92 ARG 0.013 0.001 ARG D 19 ********************** 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 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.512 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 96 ARG cc_start: 0.6808 (mtp85) cc_final: 0.6453 (mtm-85) REVERT: K 34 MET cc_start: 0.7595 (mmt) cc_final: 0.7318 (mmm) outliers start: 3 outliers final: 4 residues processed: 104 average time/residue: 2.0325 time to fit residues: 219.2476 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 : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 7 ASN 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: 0.8980 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.133994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121428 restraints weight = 17147.611| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.82 r_work: 0.3657 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3635 Z= 0.221 Angle : 0.594 10.436 4930 Z= 0.310 Chirality : 0.046 0.156 529 Planarity : 0.005 0.047 650 Dihedral : 4.561 15.520 505 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: -0.66 (0.40), residues: 457 helix: -1.64 (1.45), residues: 13 sheet: -0.27 (0.36), residues: 209 loop : -0.39 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 101 HIS 0.001 0.000 HIS B 77 PHE 0.007 0.001 PHE B 165 TYR 0.017 0.001 TYR B 143 ARG 0.012 0.001 ARG D 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6490.18 seconds wall clock time: 110 minutes 28.59 seconds (6628.59 seconds total)