Starting phenix.real_space_refine on Wed Feb 12 00:30:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rlb_19337/02_2025/8rlb_19337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rlb_19337/02_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_19337/02_2025/8rlb_19337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rlb_19337/02_2025/8rlb_19337.map" model { file = "/net/cci-nas-00/data/ceres_data/8rlb_19337/02_2025/8rlb_19337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rlb_19337/02_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-5592/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: 4.52, per 1000 atoms: 0.66 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: 1.83 Conformation dependent library (CDL) restraints added in 636.6 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 832 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 6 sheets defined 6.9% alpha, 43.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 56 through 65 removed outlier: 3.816A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'D' and resid 83 through 88 removed outlier: 4.464A pdb=" N ALA D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 22 removed outlier: 5.496A pdb=" N ASN B 149 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS B 166 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 161 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.145A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'K' and resid 30 through 31 removed outlier: 3.881A pdb=" N SER K 30 " --> pdb=" O TYR K 101 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR K 101 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG K 33 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 30 through 31 removed outlier: 3.881A pdb=" N SER K 30 " --> pdb=" O TYR K 101 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR K 101 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR K 98 " --> pdb=" O TYR K 114 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR K 114 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR K 100 " --> pdb=" O ASP K 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP K 112 " --> pdb=" O THR K 100 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.11 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: 2.750 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.570 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- 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 : 0.476 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: 2.0490 time to fit residues: 220.4285 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 : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 40 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.146020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.134064 restraints weight = 17141.019| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.90 r_work: 0.3839 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3635 Z= 0.248 Angle : 0.572 5.809 4930 Z= 0.301 Chirality : 0.047 0.170 529 Planarity : 0.004 0.041 650 Dihedral : 4.101 13.707 505 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 12.97 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.41), residues: 457 helix: -0.01 (1.54), residues: 13 sheet: 0.36 (0.36), residues: 211 loop : 0.14 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 36 HIS 0.006 0.001 HIS B 181 PHE 0.012 0.002 PHE B 84 TYR 0.012 0.001 TYR B 143 ARG 0.005 0.001 ARG D 71 *********************** 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 : 0.555 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: 1.9300 time to fit residues: 222.0516 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 : 0.531 ------------------------------------------------------------------------------- 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: 0.0980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.138421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.126705 restraints weight = 17040.002| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.77 r_work: 0.3728 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3635 Z= 0.276 Angle : 0.565 5.850 4930 Z= 0.303 Chirality : 0.046 0.162 529 Planarity : 0.004 0.048 650 Dihedral : 4.465 15.495 505 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.89 % Allowed : 16.76 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.40), residues: 457 helix: -0.26 (1.59), residues: 13 sheet: 0.16 (0.36), residues: 211 loop : -0.09 (0.41), residues: 233 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 0.019 0.002 TYR B 143 ARG 0.003 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 : 0.496 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: 0.7344 (mtp-110) cc_final: 0.7063 (mtm-85) REVERT: D 17 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8390 (m) REVERT: K 34 MET cc_start: 0.7648 (mmt) cc_final: 0.7336 (mmm) outliers start: 7 outliers final: 3 residues processed: 105 average time/residue: 1.9392 time to fit residues: 211.2456 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 : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain K residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** 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 = 0.3903 r_free = 0.3903 target = 0.133300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.120707 restraints weight = 17448.507| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.83 r_work: 0.3642 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3635 Z= 0.381 Angle : 0.626 6.863 4930 Z= 0.336 Chirality : 0.048 0.161 529 Planarity : 0.005 0.055 650 Dihedral : 4.862 16.143 505 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.43 % Allowed : 18.65 % Favored : 78.92 % 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: -0.48 (0.39), residues: 457 helix: -1.40 (1.42), residues: 13 sheet: -0.03 (0.36), residues: 212 loop : -0.42 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 115 HIS 0.004 0.001 HIS B 181 PHE 0.018 0.002 PHE K 67 TYR 0.012 0.002 TYR B 92 ARG 0.005 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 108 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.520 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: 0.7773 (mt0) cc_final: 0.7441 (mp10) REVERT: D 17 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8520 (m) REVERT: D 82 MET cc_start: 0.7465 (mmm) cc_final: 0.7147 (mmm) REVERT: K 34 MET cc_start: 0.7727 (mmt) cc_final: 0.7424 (mmm) outliers start: 9 outliers final: 5 residues processed: 105 average time/residue: 2.0019 time to fit residues: 217.7802 Evaluate side-chains 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 48 VAL 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: 0.0970 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 148 HIS ** B 159 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 = 0.3937 r_free = 0.3937 target = 0.135968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.123859 restraints weight = 17223.337| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.77 r_work: 0.3691 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3635 Z= 0.183 Angle : 0.535 5.054 4930 Z= 0.284 Chirality : 0.046 0.159 529 Planarity : 0.004 0.048 650 Dihedral : 4.444 16.107 505 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.08 % Allowed : 21.08 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.40), residues: 457 helix: -1.30 (1.47), residues: 13 sheet: 0.03 (0.37), residues: 209 loop : -0.31 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 115 HIS 0.002 0.001 HIS B 181 PHE 0.007 0.001 PHE B 46 TYR 0.016 0.001 TYR B 143 ARG 0.004 0.001 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: 4 poor density : 95 time to evaluate : 0.483 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: 0.8806 (OUTLIER) cc_final: 0.8551 (m) REVERT: K 34 MET cc_start: 0.7864 (mmt) cc_final: 0.7576 (mmm) outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 1.8800 time to fit residues: 189.3469 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 : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain D residue 17 SER 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: 0.6980 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 43 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3899 r_free = 0.3899 target = 0.132691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120283 restraints weight = 17406.208| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.81 r_work: 0.3644 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3635 Z= 0.308 Angle : 0.586 6.113 4930 Z= 0.311 Chirality : 0.047 0.156 529 Planarity : 0.005 0.049 650 Dihedral : 4.710 17.297 505 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.62 % Allowed : 21.62 % Favored : 76.76 % 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: -1.73 (1.36), residues: 13 sheet: -0.19 (0.36), residues: 213 loop : -0.50 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 115 HIS 0.003 0.001 HIS B 181 PHE 0.012 0.002 PHE K 67 TYR 0.017 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 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.535 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: B 207 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8801 (mp) REVERT: D 17 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8646 (m) REVERT: K 34 MET cc_start: 0.7908 (mmt) cc_final: 0.7621 (mmm) outliers start: 6 outliers final: 2 residues processed: 101 average time/residue: 2.0370 time to fit residues: 213.0264 Evaluate side-chains 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 LEU 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: 0.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 40 optimal weight: 0.0870 chunk 33 optimal weight: 0.0020 overall best weight: 0.3366 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.134665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122142 restraints weight = 17069.180| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.91 r_work: 0.3666 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3635 Z= 0.200 Angle : 0.555 6.291 4930 Z= 0.290 Chirality : 0.046 0.154 529 Planarity : 0.004 0.047 650 Dihedral : 4.504 16.906 505 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.35 % Allowed : 22.43 % 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 (0.40), residues: 457 helix: -1.64 (1.41), residues: 13 sheet: -0.18 (0.36), residues: 212 loop : -0.44 (0.41), residues: 232 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 0.007 0.001 PHE K 67 TYR 0.014 0.001 TYR B 143 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 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.576 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: D 17 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8571 (m) REVERT: K 34 MET cc_start: 0.7667 (mmt) cc_final: 0.7363 (mmm) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 2.0614 time to fit residues: 213.5573 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 : 0.495 ------------------------------------------------------------------------------- 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: 0.9980 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.131331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.118901 restraints weight = 17338.555| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.77 r_work: 0.3621 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3635 Z= 0.362 Angle : 0.640 6.735 4930 Z= 0.336 Chirality : 0.048 0.157 529 Planarity : 0.005 0.051 650 Dihedral : 4.919 17.795 505 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.35 % Allowed : 22.43 % 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: -0.84 (0.39), residues: 457 helix: -1.86 (1.36), residues: 13 sheet: -0.35 (0.36), residues: 214 loop : -0.56 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 115 HIS 0.003 0.001 HIS B 169 PHE 0.013 0.002 PHE B 223 TYR 0.023 0.002 TYR B 92 ARG 0.012 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: 5 poor density : 98 time to evaluate : 0.572 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: 0.7892 (mmt) cc_final: 0.7608 (mmm) outliers start: 5 outliers final: 3 residues processed: 101 average time/residue: 2.1232 time to fit residues: 222.1747 Evaluate side-chains 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain K residue 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: 0.6980 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.0770 chunk 33 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- 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 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** D 95 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 = 0.3916 r_free = 0.3916 target = 0.134402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122042 restraints weight = 17462.546| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.82 r_work: 0.3662 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3635 Z= 0.208 Angle : 0.605 8.869 4930 Z= 0.313 Chirality : 0.046 0.157 529 Planarity : 0.005 0.049 650 Dihedral : 4.679 17.518 505 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.54 % Allowed : 25.14 % Favored : 74.32 % 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: -1.84 (1.38), residues: 13 sheet: -0.45 (0.35), residues: 220 loop : -0.21 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 101 HIS 0.002 0.001 HIS B 181 PHE 0.007 0.001 PHE B 165 TYR 0.017 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 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.523 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: K 34 MET cc_start: 0.7626 (mmt) cc_final: 0.7343 (mmm) REVERT: K 117 GLN cc_start: 0.7649 (pm20) cc_final: 0.7354 (pm20) outliers start: 2 outliers final: 2 residues processed: 102 average time/residue: 2.0858 time to fit residues: 220.1952 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 : 0.589 ------------------------------------------------------------------------------- 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: 0.6980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.0970 chunk 18 optimal weight: 0.0980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** D 95 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 = 0.3910 r_free = 0.3910 target = 0.133868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.121369 restraints weight = 17550.868| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.83 r_work: 0.3654 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3635 Z= 0.243 Angle : 0.623 10.126 4930 Z= 0.322 Chirality : 0.046 0.156 529 Planarity : 0.005 0.047 650 Dihedral : 4.647 17.540 505 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.27 % Allowed : 26.22 % Favored : 73.51 % 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: -0.69 (0.39), residues: 457 helix: -1.66 (1.42), residues: 13 sheet: -0.26 (0.36), 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 0.002 0.001 HIS B 181 PHE 0.008 0.002 PHE B 46 TYR 0.018 0.002 TYR B 143 ARG 0.012 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 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.568 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: K 34 MET cc_start: 0.7660 (mmt) cc_final: 0.7354 (mmm) REVERT: K 117 GLN cc_start: 0.7680 (pm20) cc_final: 0.7410 (pm20) outliers start: 1 outliers final: 2 residues processed: 99 average time/residue: 2.0132 time to fit residues: 206.4070 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 : 0.539 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 chunk 24 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** D 95 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 = 0.3912 r_free = 0.3912 target = 0.133943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121596 restraints weight = 17327.258| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.78 r_work: 0.3654 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3635 Z= 0.241 Angle : 0.628 10.154 4930 Z= 0.322 Chirality : 0.046 0.154 529 Planarity : 0.005 0.048 650 Dihedral : 4.645 17.730 505 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.27 % Allowed : 26.49 % Favored : 73.24 % 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: -0.68 (0.39), residues: 457 helix: -1.68 (1.40), residues: 13 sheet: -0.26 (0.36), residues: 210 loop : -0.43 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 101 HIS 0.002 0.001 HIS B 181 PHE 0.007 0.001 PHE D 27 TYR 0.014 0.001 TYR B 143 ARG 0.013 0.001 ARG D 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6277.68 seconds wall clock time: 110 minutes 32.46 seconds (6632.46 seconds total)