Starting phenix.real_space_refine on Fri Jul 25 01:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rlb_19337/07_2025/8rlb_19337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rlb_19337/07_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_19337/07_2025/8rlb_19337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rlb_19337/07_2025/8rlb_19337.map" model { file = "/net/cci-nas-00/data/ceres_data/8rlb_19337/07_2025/8rlb_19337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rlb_19337/07_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-5711/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: 4.37, per 1000 atoms: 0.63 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: 1.65 Conformation dependent library (CDL) restraints added in 642.5 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: 0.62 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: 2.21 Time building geometry restraints manager: 2.06 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: 3.850 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: 0.130 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.490 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.820 ------------------------------------------------------------------------------- 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 : 0.490 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: 2.1348 time to fit residues: 230.5415 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 : 0.571 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.134064 restraints weight = 17140.979| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.90 r_work: 0.3838 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 13.708 505 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 : 0.518 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: 1.9950 time to fit residues: 230.3636 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 : 0.614 ------------------------------------------------------------------------------- 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: 0.6980 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.0030 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.138319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.126602 restraints weight = 17061.517| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.76 r_work: 0.3732 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3409 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= 0.183 Angle : 0.563 5.735 4934 Z= 0.302 Chirality : 0.046 0.162 529 Planarity : 0.004 0.048 650 Dihedral : 4.481 15.570 505 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.62 % Allowed : 17.30 % Favored : 81.08 % 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: -0.01 (0.40), residues: 457 helix: -0.33 (1.55), residues: 13 sheet: 0.24 (0.36), residues: 208 loop : -0.10 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 115 HIS 0.003 0.001 HIS B 181 PHE 0.019 0.002 PHE K 67 TYR 0.017 0.002 TYR B 143 ARG 0.003 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 156) hydrogen bonds : angle 6.27403 ( 396) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.20870 ( 4) covalent geometry : bond 0.00415 ( 3635) covalent geometry : angle 0.56183 ( 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 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.485 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 168 ARG cc_start: 0.7326 (mtp-110) cc_final: 0.7038 (mtm-85) REVERT: D 17 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8400 (m) REVERT: K 34 MET cc_start: 0.7662 (mmt) cc_final: 0.7342 (mmm) outliers start: 6 outliers final: 2 residues processed: 104 average time/residue: 1.8726 time to fit residues: 201.9347 Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.135784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.123808 restraints weight = 17639.754| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.77 r_work: 0.3686 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3637 Z= 0.192 Angle : 0.568 6.054 4934 Z= 0.303 Chirality : 0.046 0.159 529 Planarity : 0.005 0.047 650 Dihedral : 4.537 15.969 505 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.35 % Allowed : 19.19 % Favored : 79.46 % 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: -0.38 (0.39), residues: 457 helix: -0.93 (1.50), residues: 13 sheet: -0.03 (0.36), residues: 210 loop : -0.31 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 115 HIS 0.004 0.001 HIS B 181 PHE 0.014 0.002 PHE K 67 TYR 0.015 0.002 TYR B 143 ARG 0.003 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 156) hydrogen bonds : angle 6.22665 ( 396) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.89490 ( 4) covalent geometry : bond 0.00447 ( 3635) covalent geometry : angle 0.56795 ( 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 100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.696 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: 0.7742 (mt0) cc_final: 0.7402 (mp10) REVERT: D 17 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8441 (m) REVERT: K 34 MET cc_start: 0.7687 (mmt) cc_final: 0.7384 (mmm) outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 2.1245 time to fit residues: 215.9506 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 : 0.853 ------------------------------------------------------------------------------- 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: 0.2980 chunk 7 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.0170 chunk 33 optimal weight: 0.0030 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 overall best weight: 0.1628 ------------------------------------------------------------------------------- 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 204 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 = 0.3988 r_free = 0.3988 target = 0.140394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.128020 restraints weight = 16992.296| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.87 r_work: 0.3732 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3637 Z= 0.100 Angle : 0.509 5.089 4934 Z= 0.270 Chirality : 0.045 0.156 529 Planarity : 0.004 0.043 650 Dihedral : 4.186 15.538 505 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.54 % Allowed : 20.00 % Favored : 79.46 % 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: -0.13 (0.40), residues: 457 helix: -0.63 (1.59), residues: 13 sheet: 0.13 (0.36), residues: 206 loop : -0.13 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 101 HIS 0.002 0.001 HIS B 181 PHE 0.007 0.001 PHE B 114 TYR 0.023 0.001 TYR B 143 ARG 0.005 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.02743 ( 156) hydrogen bonds : angle 6.01635 ( 396) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.33829 ( 4) covalent geometry : bond 0.00229 ( 3635) covalent geometry : angle 0.50951 ( 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 97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.516 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: 0.8633 (t) cc_final: 0.8384 (m) REVERT: K 34 MET cc_start: 0.7567 (mmt) cc_final: 0.7308 (mmm) outliers start: 2 outliers final: 2 residues processed: 96 average time/residue: 1.8587 time to fit residues: 185.0734 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 : 0.482 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.133210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.120757 restraints weight = 17381.159| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.83 r_work: 0.3643 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3637 Z= 0.230 Angle : 0.611 6.356 4934 Z= 0.325 Chirality : 0.047 0.158 529 Planarity : 0.005 0.051 650 Dihedral : 4.701 17.437 505 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.35 % Allowed : 21.62 % 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: -0.50 (0.40), residues: 457 helix: -1.29 (1.46), residues: 13 sheet: -0.14 (0.37), residues: 210 loop : -0.33 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 115 HIS 0.004 0.001 HIS B 181 PHE 0.014 0.002 PHE K 67 TYR 0.018 0.002 TYR B 92 ARG 0.005 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 156) hydrogen bonds : angle 6.34982 ( 396) SS BOND : bond 0.00492 ( 2) SS BOND : angle 1.12542 ( 4) covalent geometry : bond 0.00536 ( 3635) covalent geometry : angle 0.61074 ( 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 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.485 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 166 LYS cc_start: 0.8204 (mttp) cc_final: 0.7774 (mttp) REVERT: B 178 LEU cc_start: 0.7847 (mm) cc_final: 0.7638 (mt) REVERT: B 180 ASP cc_start: 0.6597 (m-30) cc_final: 0.6290 (m-30) REVERT: D 17 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8569 (m) REVERT: K 34 MET cc_start: 0.7685 (mmt) cc_final: 0.7385 (mmm) outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 2.0195 time to fit residues: 215.5874 Evaluate side-chains 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 107 LYS 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: 0.6980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 24 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.0070 overall best weight: 0.2536 ------------------------------------------------------------------------------- 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.135848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.123397 restraints weight = 17073.068| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.89 r_work: 0.3681 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 : 0.003 0.021 3637 Z= 0.118 Angle : 0.540 5.792 4934 Z= 0.284 Chirality : 0.046 0.154 529 Planarity : 0.005 0.045 650 Dihedral : 4.390 16.394 505 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.35 % Allowed : 21.62 % 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: -0.45 (0.39), residues: 457 helix: -1.27 (1.51), residues: 13 sheet: -0.13 (0.36), residues: 209 loop : -0.26 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 101 HIS 0.002 0.000 HIS B 181 PHE 0.006 0.001 PHE B 114 TYR 0.018 0.001 TYR B 143 ARG 0.006 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.02851 ( 156) hydrogen bonds : angle 6.20588 ( 396) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.34666 ( 4) covalent geometry : bond 0.00272 ( 3635) covalent geometry : angle 0.54023 ( 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 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.475 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 166 LYS cc_start: 0.8184 (mttp) cc_final: 0.7714 (mttp) REVERT: B 180 ASP cc_start: 0.6566 (m-30) cc_final: 0.6247 (m-30) REVERT: D 17 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8527 (m) REVERT: K 34 MET cc_start: 0.7631 (mmt) cc_final: 0.7365 (mmm) REVERT: K 117 GLN cc_start: 0.7651 (pm20) cc_final: 0.7348 (pm20) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 1.9891 time to fit residues: 205.9171 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 : 0.499 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 159 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.119206 restraints weight = 17392.947| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.94 r_work: 0.3618 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3637 Z= 0.230 Angle : 0.621 6.288 4934 Z= 0.328 Chirality : 0.047 0.153 529 Planarity : 0.005 0.050 650 Dihedral : 4.798 17.174 505 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.08 % Allowed : 23.24 % Favored : 75.68 % 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: -0.77 (0.39), residues: 457 helix: -1.74 (1.38), residues: 13 sheet: -0.33 (0.36), residues: 211 loop : -0.48 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 115 HIS 0.002 0.001 HIS B 181 PHE 0.012 0.002 PHE B 223 TYR 0.023 0.002 TYR B 92 ARG 0.011 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 156) hydrogen bonds : angle 6.43080 ( 396) SS BOND : bond 0.00641 ( 2) SS BOND : angle 1.09744 ( 4) covalent geometry : bond 0.00536 ( 3635) covalent geometry : angle 0.62021 ( 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 100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 2.014 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: B 69 GLN cc_start: 0.7766 (mt0) cc_final: 0.7439 (mp10) REVERT: B 166 LYS cc_start: 0.8217 (mttp) cc_final: 0.7703 (mttp) REVERT: B 180 ASP cc_start: 0.6543 (m-30) cc_final: 0.6215 (m-30) REVERT: K 34 MET cc_start: 0.7659 (mmt) cc_final: 0.7353 (mmm) REVERT: K 117 GLN cc_start: 0.7763 (pm20) cc_final: 0.7473 (pm20) outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 2.6170 time to fit residues: 267.0993 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 : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 0 optimal weight: 0.8980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.133960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.121325 restraints weight = 17400.181| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.85 r_work: 0.3651 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5124 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= 0.160 Angle : 0.587 6.933 4934 Z= 0.305 Chirality : 0.046 0.155 529 Planarity : 0.005 0.048 650 Dihedral : 4.618 17.674 505 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.54 % Allowed : 24.32 % 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: -0.75 (0.39), residues: 457 helix: -1.73 (1.38), residues: 13 sheet: -0.55 (0.35), residues: 220 loop : -0.17 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 101 HIS 0.003 0.001 HIS B 181 PHE 0.008 0.001 PHE B 223 TYR 0.014 0.001 TYR B 92 ARG 0.011 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 156) hydrogen bonds : angle 6.34443 ( 396) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.54749 ( 4) covalent geometry : bond 0.00374 ( 3635) covalent geometry : angle 0.58679 ( 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 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.881 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 166 LYS cc_start: 0.8225 (mttp) cc_final: 0.7698 (mttp) REVERT: B 180 ASP cc_start: 0.6502 (m-30) cc_final: 0.6171 (m-30) REVERT: K 34 MET cc_start: 0.7606 (mmt) cc_final: 0.7332 (mmm) outliers start: 2 outliers final: 2 residues processed: 97 average time/residue: 2.7371 time to fit residues: 276.3372 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 : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.132662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.120041 restraints weight = 17451.640| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.85 r_work: 0.3633 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3637 Z= 0.197 Angle : 0.631 9.382 4934 Z= 0.328 Chirality : 0.047 0.155 529 Planarity : 0.005 0.049 650 Dihedral : 4.765 17.276 505 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.27 % Allowed : 24.86 % 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: -0.73 (0.39), residues: 457 helix: -1.71 (1.40), residues: 13 sheet: -0.32 (0.35), residues: 210 loop : -0.44 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 101 HIS 0.003 0.001 HIS B 181 PHE 0.010 0.002 PHE B 223 TYR 0.019 0.002 TYR B 92 ARG 0.013 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 156) hydrogen bonds : angle 6.41033 ( 396) SS BOND : bond 0.00465 ( 2) SS BOND : angle 0.96318 ( 4) covalent geometry : bond 0.00464 ( 3635) covalent geometry : angle 0.63088 ( 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 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.666 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: B 69 GLN cc_start: 0.7689 (mt0) cc_final: 0.7440 (mp10) REVERT: B 166 LYS cc_start: 0.8241 (mttp) cc_final: 0.7822 (mttp) REVERT: K 34 MET cc_start: 0.7610 (mmt) cc_final: 0.7339 (mmm) REVERT: K 117 GLN cc_start: 0.7712 (pm20) cc_final: 0.7447 (pm20) outliers start: 1 outliers final: 2 residues processed: 103 average time/residue: 2.3157 time to fit residues: 249.5427 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 : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 33 optimal weight: 0.0070 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.134692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122507 restraints weight = 17037.592| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.74 r_work: 0.3657 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3637 Z= 0.149 Angle : 0.612 10.033 4934 Z= 0.313 Chirality : 0.046 0.158 529 Planarity : 0.005 0.047 650 Dihedral : 4.625 17.288 505 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.54 % Allowed : 25.68 % Favored : 73.78 % 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 (0.39), residues: 457 helix: -1.59 (1.41), residues: 13 sheet: -0.29 (0.36), residues: 210 loop : -0.38 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 101 HIS 0.002 0.001 HIS B 181 PHE 0.007 0.001 PHE B 46 TYR 0.014 0.001 TYR B 143 ARG 0.012 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 156) hydrogen bonds : angle 6.31718 ( 396) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.65639 ( 4) covalent geometry : bond 0.00350 ( 3635) covalent geometry : angle 0.61201 ( 4930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7527.37 seconds wall clock time: 135 minutes 15.23 seconds (8115.23 seconds total)