Starting phenix.real_space_refine on Tue Mar 3 12:25:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk0_25168/03_2026/7sk0_25168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk0_25168/03_2026/7sk0_25168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sk0_25168/03_2026/7sk0_25168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk0_25168/03_2026/7sk0_25168.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sk0_25168/03_2026/7sk0_25168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk0_25168/03_2026/7sk0_25168.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.264 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 K 5 8.98 5 S 16 5.16 5 C 2781 2.51 5 N 654 2.21 5 O 712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4168 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2074 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2073 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 13 Unusual residues: {' K': 5, 'OCT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'OCT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.07, per 1000 atoms: 0.26 Number of scatterers: 4168 At special positions: 0 Unit cell: (69.357, 69.357, 90.96, 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) K 5 19.00 S 16 16.00 O 712 8.00 N 654 7.00 C 2781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 69 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 157.6 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 24 through 67 removed outlier: 4.087A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 127 through 161 removed outlier: 3.528A pdb=" N ILE A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 3.592A pdb=" N VAL A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 173 removed outlier: 3.755A pdb=" N VAL A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 196 removed outlier: 3.543A pdb=" N ALA A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.771A pdb=" N SER A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 270 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'B' and resid 25 through 67 removed outlier: 4.087A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 127 through 161 removed outlier: 3.529A pdb=" N ILE B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Proline residue: B 143 - end of helix removed outlier: 3.592A pdb=" N VAL B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 173 removed outlier: 3.754A pdb=" N VAL B 165 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 196 removed outlier: 3.542A pdb=" N ALA B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.770A pdb=" N SER B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 270 Processing helix chain 'B' and resid 270 through 280 315 hydrogen bonds defined for protein. 945 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: 0.47 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1250 1.34 - 1.46: 1152 1.46 - 1.58: 1854 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 4276 Sorted by residual: bond pdb=" CG LEU B 79 " pdb=" CD1 LEU B 79 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.34e+00 bond pdb=" CG LEU A 79 " pdb=" CD1 LEU A 79 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.30e+00 bond pdb=" CG1 ILE A 258 " pdb=" CD1 ILE A 258 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.25e+00 bond pdb=" CG1 ILE B 258 " pdb=" CD1 ILE B 258 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.14e+00 bond pdb=" CB GLU A 207 " pdb=" CG GLU A 207 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.64e+00 ... (remaining 4271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 5205 1.62 - 3.24: 472 3.24 - 4.86: 98 4.86 - 6.47: 22 6.47 - 8.09: 2 Bond angle restraints: 5799 Sorted by residual: angle pdb=" N ASP B 103 " pdb=" CA ASP B 103 " pdb=" C ASP B 103 " ideal model delta sigma weight residual 109.24 103.89 5.35 1.51e+00 4.39e-01 1.26e+01 angle pdb=" N ASP A 103 " pdb=" CA ASP A 103 " pdb=" C ASP A 103 " ideal model delta sigma weight residual 109.24 103.91 5.33 1.51e+00 4.39e-01 1.25e+01 angle pdb=" C ASN A 95 " pdb=" N ALA A 96 " pdb=" CA ALA A 96 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C ASN B 95 " pdb=" N ALA B 96 " pdb=" CA ALA B 96 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C TRP A 100 " pdb=" N ASN A 101 " pdb=" CA ASN A 101 " ideal model delta sigma weight residual 120.38 124.45 -4.07 1.37e+00 5.33e-01 8.84e+00 ... (remaining 5794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2155 15.79 - 31.57: 222 31.57 - 47.36: 40 47.36 - 63.15: 14 63.15 - 78.94: 8 Dihedral angle restraints: 2439 sinusoidal: 951 harmonic: 1488 Sorted by residual: dihedral pdb=" N ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " pdb=" CG ASN B 87 " ideal model delta sinusoidal sigma weight residual -60.00 -113.65 53.65 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " pdb=" CG ASN A 87 " ideal model delta sinusoidal sigma weight residual -60.00 -113.62 53.62 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" CB MET A 279 " pdb=" CG MET A 279 " pdb=" SD MET A 279 " pdb=" CE MET A 279 " ideal model delta sinusoidal sigma weight residual -180.00 -127.29 -52.71 3 1.50e+01 4.44e-03 9.14e+00 ... (remaining 2436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 378 0.039 - 0.078: 160 0.078 - 0.117: 86 0.117 - 0.156: 22 0.156 - 0.194: 12 Chirality restraints: 658 Sorted by residual: chirality pdb=" CB VAL A 92 " pdb=" CA VAL A 92 " pdb=" CG1 VAL A 92 " pdb=" CG2 VAL A 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CG LEU A 254 " pdb=" CB LEU A 254 " pdb=" CD1 LEU A 254 " pdb=" CD2 LEU A 254 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CG LEU B 254 " pdb=" CB LEU B 254 " pdb=" CD1 LEU B 254 " pdb=" CD2 LEU B 254 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 655 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 254 " 0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C LEU A 254 " -0.077 2.00e-02 2.50e+03 pdb=" O LEU A 254 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 255 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 254 " -0.022 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C LEU B 254 " 0.076 2.00e-02 2.50e+03 pdb=" O LEU B 254 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 255 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 80 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLY A 80 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY A 80 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 81 " 0.019 2.00e-02 2.50e+03 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.63: 38 2.63 - 3.26: 4786 3.26 - 3.89: 8391 3.89 - 4.51: 11197 4.51 - 5.14: 16862 Nonbonded interactions: 41274 Sorted by model distance: nonbonded pdb=" OG SER B 71 " pdb=" OE1 GLN B 74 " model vdw 2.005 3.040 nonbonded pdb=" OG SER A 71 " pdb=" OE1 GLN A 74 " model vdw 2.005 3.040 nonbonded pdb=" ND2 ASN A 87 " pdb=" O GLY B 229 " model vdw 2.141 3.120 nonbonded pdb=" O GLY A 229 " pdb=" ND2 ASN B 87 " model vdw 2.230 3.120 nonbonded pdb=" O SER B 116 " pdb=" OG1 THR B 117 " model vdw 2.270 3.040 ... (remaining 41269 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 279 or (resid 280 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2)) or resid 401)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 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 : 0.009 0.080 4277 Z= 0.360 Angle : 1.042 8.092 5801 Z= 0.587 Chirality : 0.058 0.194 658 Planarity : 0.008 0.044 712 Dihedral : 14.222 78.936 1484 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.44 % Allowed : 1.33 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.36), residues: 510 helix: 0.73 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -1.30 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 163 TYR 0.031 0.005 TYR A 237 PHE 0.039 0.004 PHE B 144 TRP 0.010 0.002 TRP A 100 HIS 0.013 0.003 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00864 ( 4276) covalent geometry : angle 1.04187 ( 5799) SS BOND : bond 0.00685 ( 1) SS BOND : angle 1.60616 ( 2) hydrogen bonds : bond 0.20411 ( 315) hydrogen bonds : angle 7.80640 ( 945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7034 (mp10) cc_final: 0.6579 (mp10) REVERT: B 28 LEU cc_start: 0.8156 (mt) cc_final: 0.7842 (mt) REVERT: B 74 GLN cc_start: 0.7280 (mp10) cc_final: 0.6809 (mp10) REVERT: B 87 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6933 (t0) REVERT: B 243 GLU cc_start: 0.7398 (mp0) cc_final: 0.7169 (mp0) outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 0.0434 time to fit residues: 6.1702 Evaluate side-chains 87 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.218559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.171226 restraints weight = 5329.019| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.65 r_work: 0.3898 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4277 Z= 0.202 Angle : 0.689 5.981 5801 Z= 0.377 Chirality : 0.045 0.194 658 Planarity : 0.005 0.028 712 Dihedral : 4.913 22.640 570 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.43 % Allowed : 6.64 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.39), residues: 510 helix: 1.82 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -0.68 (0.78), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 81 TYR 0.014 0.002 TYR A 88 PHE 0.020 0.002 PHE A 144 TRP 0.005 0.001 TRP A 210 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 4276) covalent geometry : angle 0.68949 ( 5799) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.26195 ( 2) hydrogen bonds : bond 0.05665 ( 315) hydrogen bonds : angle 5.19350 ( 945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7418 (mp10) cc_final: 0.6956 (mp10) REVERT: A 243 GLU cc_start: 0.7535 (mp0) cc_final: 0.7160 (mp0) REVERT: A 260 MET cc_start: 0.7627 (mmm) cc_final: 0.7421 (mmt) REVERT: A 276 PHE cc_start: 0.6666 (t80) cc_final: 0.6382 (t80) REVERT: A 279 MET cc_start: 0.3304 (ttt) cc_final: 0.2930 (ttp) REVERT: B 28 LEU cc_start: 0.8212 (mt) cc_final: 0.7917 (mt) REVERT: B 49 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B 74 GLN cc_start: 0.7396 (mp10) cc_final: 0.6875 (mp10) REVERT: B 189 PHE cc_start: 0.5715 (m-10) cc_final: 0.5381 (m-10) outliers start: 11 outliers final: 9 residues processed: 105 average time/residue: 0.0411 time to fit residues: 6.1938 Evaluate side-chains 102 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.220990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173659 restraints weight = 5235.780| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.65 r_work: 0.3914 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4277 Z= 0.163 Angle : 0.615 7.333 5801 Z= 0.331 Chirality : 0.043 0.191 658 Planarity : 0.004 0.029 712 Dihedral : 4.740 20.202 568 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.65 % Allowed : 7.52 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.40), residues: 510 helix: 2.00 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -0.76 (0.81), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.012 0.001 TYR A 88 PHE 0.014 0.002 PHE A 174 TRP 0.009 0.001 TRP B 100 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4276) covalent geometry : angle 0.61501 ( 5799) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.21031 ( 2) hydrogen bonds : bond 0.04790 ( 315) hydrogen bonds : angle 4.74542 ( 945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7350 (mp10) cc_final: 0.6633 (mp10) REVERT: A 243 GLU cc_start: 0.7589 (mp0) cc_final: 0.7181 (mp0) REVERT: A 279 MET cc_start: 0.3321 (ttt) cc_final: 0.2934 (ttp) REVERT: B 49 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7416 (tm-30) REVERT: B 74 GLN cc_start: 0.7423 (mp10) cc_final: 0.6681 (mp10) outliers start: 12 outliers final: 11 residues processed: 99 average time/residue: 0.0427 time to fit residues: 6.1290 Evaluate side-chains 104 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.221826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.174374 restraints weight = 5259.016| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.69 r_work: 0.3925 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4277 Z= 0.153 Angle : 0.582 6.676 5801 Z= 0.319 Chirality : 0.041 0.191 658 Planarity : 0.004 0.032 712 Dihedral : 4.658 21.930 568 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.43 % Allowed : 10.40 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.39), residues: 510 helix: 2.05 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -0.75 (0.81), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.009 0.001 TYR B 88 PHE 0.014 0.002 PHE B 174 TRP 0.006 0.001 TRP B 100 HIS 0.002 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4276) covalent geometry : angle 0.58222 ( 5799) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.14788 ( 2) hydrogen bonds : bond 0.04464 ( 315) hydrogen bonds : angle 4.61085 ( 945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8583 (tp) cc_final: 0.8286 (mm) REVERT: A 74 GLN cc_start: 0.7389 (mp10) cc_final: 0.6709 (mp10) REVERT: A 231 TYR cc_start: 0.6420 (m-80) cc_final: 0.6096 (m-80) REVERT: A 243 GLU cc_start: 0.7550 (mp0) cc_final: 0.7125 (mp0) REVERT: A 279 MET cc_start: 0.3042 (ttt) cc_final: 0.2674 (ttp) REVERT: B 49 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7438 (tm-30) REVERT: B 56 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7515 (tt) REVERT: B 74 GLN cc_start: 0.7429 (mp10) cc_final: 0.6727 (mp10) REVERT: B 260 MET cc_start: 0.7712 (mmt) cc_final: 0.7420 (mmm) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.0388 time to fit residues: 5.7814 Evaluate side-chains 103 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.0030 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 25 optimal weight: 0.0870 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.222368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.174706 restraints weight = 5312.195| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.75 r_work: 0.3924 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4277 Z= 0.144 Angle : 0.566 5.853 5801 Z= 0.311 Chirality : 0.040 0.191 658 Planarity : 0.004 0.032 712 Dihedral : 4.510 22.433 568 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.65 % Allowed : 11.50 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.38), residues: 510 helix: 2.12 (0.24), residues: 412 sheet: None (None), residues: 0 loop : -0.65 (0.81), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.011 0.001 TYR A 252 PHE 0.014 0.001 PHE B 174 TRP 0.006 0.001 TRP B 100 HIS 0.001 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4276) covalent geometry : angle 0.56567 ( 5799) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.31194 ( 2) hydrogen bonds : bond 0.04255 ( 315) hydrogen bonds : angle 4.60231 ( 945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8516 (tp) cc_final: 0.8234 (mm) REVERT: A 56 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7190 (tt) REVERT: A 74 GLN cc_start: 0.7332 (mp10) cc_final: 0.6627 (mp10) REVERT: A 231 TYR cc_start: 0.6380 (m-80) cc_final: 0.5931 (m-80) REVERT: A 243 GLU cc_start: 0.7580 (mp0) cc_final: 0.7114 (mp0) REVERT: A 279 MET cc_start: 0.3057 (ttt) cc_final: 0.2677 (ttp) REVERT: B 31 LEU cc_start: 0.8564 (tp) cc_final: 0.8296 (mm) REVERT: B 56 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7311 (tt) REVERT: B 74 GLN cc_start: 0.7400 (mp10) cc_final: 0.6668 (mp10) REVERT: B 196 PHE cc_start: 0.6797 (m-80) cc_final: 0.6516 (m-80) outliers start: 12 outliers final: 7 residues processed: 100 average time/residue: 0.0376 time to fit residues: 5.5613 Evaluate side-chains 105 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.222026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.175351 restraints weight = 5378.035| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.73 r_work: 0.3929 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4277 Z= 0.144 Angle : 0.586 6.118 5801 Z= 0.316 Chirality : 0.040 0.185 658 Planarity : 0.004 0.034 712 Dihedral : 4.440 21.465 568 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.21 % Allowed : 12.83 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.38), residues: 510 helix: 2.25 (0.24), residues: 412 sheet: None (None), residues: 0 loop : -0.62 (0.80), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.006 0.001 TYR A 252 PHE 0.014 0.001 PHE B 174 TRP 0.007 0.001 TRP B 102 HIS 0.001 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4276) covalent geometry : angle 0.58585 ( 5799) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.40798 ( 2) hydrogen bonds : bond 0.04185 ( 315) hydrogen bonds : angle 4.60311 ( 945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8457 (tp) cc_final: 0.8192 (mm) REVERT: A 56 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7216 (tt) REVERT: A 74 GLN cc_start: 0.7304 (mp10) cc_final: 0.6578 (mp10) REVERT: A 231 TYR cc_start: 0.6420 (m-80) cc_final: 0.5936 (m-80) REVERT: A 243 GLU cc_start: 0.7551 (mp0) cc_final: 0.7098 (mp0) REVERT: A 279 MET cc_start: 0.3079 (ttt) cc_final: 0.2695 (ttp) REVERT: B 31 LEU cc_start: 0.8520 (tp) cc_final: 0.8242 (mm) REVERT: B 56 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7116 (tp) REVERT: B 74 GLN cc_start: 0.7331 (mp10) cc_final: 0.6711 (mp10) REVERT: B 196 PHE cc_start: 0.6759 (m-80) cc_final: 0.6540 (m-80) outliers start: 10 outliers final: 7 residues processed: 102 average time/residue: 0.0388 time to fit residues: 5.7714 Evaluate side-chains 105 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.219159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.171641 restraints weight = 5434.112| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.74 r_work: 0.3894 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4277 Z= 0.166 Angle : 0.602 6.988 5801 Z= 0.324 Chirality : 0.042 0.193 658 Planarity : 0.004 0.036 712 Dihedral : 4.513 22.080 568 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.77 % Allowed : 13.72 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.39), residues: 510 helix: 2.13 (0.25), residues: 414 sheet: None (None), residues: 0 loop : -0.61 (0.81), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.008 0.001 TYR A 245 PHE 0.013 0.002 PHE B 174 TRP 0.006 0.001 TRP B 100 HIS 0.001 0.000 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4276) covalent geometry : angle 0.60238 ( 5799) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.37991 ( 2) hydrogen bonds : bond 0.04251 ( 315) hydrogen bonds : angle 4.74283 ( 945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8518 (tp) cc_final: 0.8214 (mm) REVERT: A 50 ASP cc_start: 0.8621 (t0) cc_final: 0.8392 (t0) REVERT: A 56 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7509 (tt) REVERT: A 74 GLN cc_start: 0.7355 (mp10) cc_final: 0.6630 (mp10) REVERT: A 231 TYR cc_start: 0.6419 (m-80) cc_final: 0.5821 (m-80) REVERT: A 243 GLU cc_start: 0.7542 (mp0) cc_final: 0.7119 (mp0) REVERT: A 279 MET cc_start: 0.3166 (ttt) cc_final: 0.2780 (ttp) REVERT: B 31 LEU cc_start: 0.8528 (tp) cc_final: 0.8243 (mm) REVERT: B 56 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7216 (tt) REVERT: B 74 GLN cc_start: 0.7409 (mp10) cc_final: 0.6722 (mp10) outliers start: 8 outliers final: 6 residues processed: 99 average time/residue: 0.0318 time to fit residues: 4.6414 Evaluate side-chains 100 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.0170 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.221451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.174822 restraints weight = 5332.198| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.72 r_work: 0.3929 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4277 Z= 0.153 Angle : 0.608 8.841 5801 Z= 0.329 Chirality : 0.043 0.244 658 Planarity : 0.004 0.037 712 Dihedral : 4.434 21.651 568 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.33 % Allowed : 15.93 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.39), residues: 510 helix: 2.20 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.67 (0.81), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.016 0.001 TYR A 30 PHE 0.013 0.001 PHE B 174 TRP 0.006 0.001 TRP A 100 HIS 0.001 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4276) covalent geometry : angle 0.60758 ( 5799) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.59454 ( 2) hydrogen bonds : bond 0.04134 ( 315) hydrogen bonds : angle 4.78332 ( 945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7480 (tt) REVERT: A 74 GLN cc_start: 0.7338 (mp10) cc_final: 0.6623 (mp10) REVERT: A 231 TYR cc_start: 0.6436 (m-80) cc_final: 0.5901 (m-80) REVERT: A 243 GLU cc_start: 0.7542 (mp0) cc_final: 0.7079 (mp0) REVERT: A 279 MET cc_start: 0.3161 (ttt) cc_final: 0.2773 (ttp) REVERT: B 31 LEU cc_start: 0.8589 (tp) cc_final: 0.8294 (mm) REVERT: B 56 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7145 (tt) REVERT: B 74 GLN cc_start: 0.7393 (mp10) cc_final: 0.6726 (mp10) outliers start: 6 outliers final: 4 residues processed: 97 average time/residue: 0.0370 time to fit residues: 5.2978 Evaluate side-chains 98 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.218625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.171133 restraints weight = 5447.336| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.77 r_work: 0.3884 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4277 Z= 0.176 Angle : 0.651 10.977 5801 Z= 0.348 Chirality : 0.044 0.241 658 Planarity : 0.004 0.034 712 Dihedral : 4.488 22.171 568 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.55 % Allowed : 15.93 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.39), residues: 510 helix: 2.06 (0.25), residues: 414 sheet: None (None), residues: 0 loop : -0.80 (0.79), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.017 0.002 TYR B 30 PHE 0.013 0.002 PHE B 174 TRP 0.005 0.001 TRP B 100 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 4276) covalent geometry : angle 0.65093 ( 5799) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.66171 ( 2) hydrogen bonds : bond 0.04238 ( 315) hydrogen bonds : angle 4.87816 ( 945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7268 (tt) REVERT: A 74 GLN cc_start: 0.7363 (mp10) cc_final: 0.6686 (mp10) REVERT: A 231 TYR cc_start: 0.6509 (m-80) cc_final: 0.5882 (m-80) REVERT: A 243 GLU cc_start: 0.7566 (mp0) cc_final: 0.7108 (mp0) REVERT: A 279 MET cc_start: 0.3152 (ttt) cc_final: 0.2776 (ttp) REVERT: B 56 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7214 (tt) REVERT: B 74 GLN cc_start: 0.7435 (mp10) cc_final: 0.6770 (mp10) REVERT: B 196 PHE cc_start: 0.6702 (m-80) cc_final: 0.6398 (m-80) outliers start: 7 outliers final: 5 residues processed: 101 average time/residue: 0.0367 time to fit residues: 5.4743 Evaluate side-chains 102 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.0570 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.223690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.177219 restraints weight = 5276.999| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.76 r_work: 0.3951 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4277 Z= 0.145 Angle : 0.647 12.593 5801 Z= 0.338 Chirality : 0.042 0.226 658 Planarity : 0.004 0.037 712 Dihedral : 4.340 22.025 568 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.33 % Allowed : 16.37 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.39), residues: 510 helix: 2.26 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.99 (0.76), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.013 0.001 TYR B 30 PHE 0.013 0.001 PHE B 133 TRP 0.008 0.001 TRP A 100 HIS 0.004 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4276) covalent geometry : angle 0.64717 ( 5799) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.84750 ( 2) hydrogen bonds : bond 0.03932 ( 315) hydrogen bonds : angle 4.73397 ( 945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7322 (tt) REVERT: A 74 GLN cc_start: 0.7395 (mp10) cc_final: 0.6728 (mp10) REVERT: A 231 TYR cc_start: 0.6404 (m-80) cc_final: 0.5910 (m-80) REVERT: A 243 GLU cc_start: 0.7544 (mp0) cc_final: 0.7061 (mp0) REVERT: A 279 MET cc_start: 0.3208 (ttt) cc_final: 0.2831 (ttp) REVERT: B 31 LEU cc_start: 0.8470 (tp) cc_final: 0.8206 (mm) REVERT: B 56 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.6914 (tt) REVERT: B 74 GLN cc_start: 0.7455 (mp10) cc_final: 0.6813 (mp10) REVERT: B 196 PHE cc_start: 0.6857 (m-80) cc_final: 0.6538 (m-80) outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 0.0467 time to fit residues: 5.9954 Evaluate side-chains 93 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 237 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.1980 chunk 4 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.224754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.177142 restraints weight = 5474.978| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.90 r_work: 0.3943 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4277 Z= 0.148 Angle : 0.664 12.595 5801 Z= 0.348 Chirality : 0.042 0.229 658 Planarity : 0.004 0.036 712 Dihedral : 4.324 21.865 568 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.11 % Allowed : 16.81 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.39), residues: 510 helix: 2.26 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -1.12 (0.75), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.014 0.001 TYR B 30 PHE 0.013 0.001 PHE B 133 TRP 0.015 0.001 TRP B 102 HIS 0.005 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4276) covalent geometry : angle 0.66445 ( 5799) SS BOND : bond 0.00094 ( 1) SS BOND : angle 0.58886 ( 2) hydrogen bonds : bond 0.03904 ( 315) hydrogen bonds : angle 4.73306 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1119.19 seconds wall clock time: 19 minutes 49.95 seconds (1189.95 seconds total)