Starting phenix.real_space_refine on Tue Feb 3 12:20:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8s_62179/02_2026/9k8s_62179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8s_62179/02_2026/9k8s_62179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k8s_62179/02_2026/9k8s_62179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8s_62179/02_2026/9k8s_62179.map" model { file = "/net/cci-nas-00/data/ceres_data/9k8s_62179/02_2026/9k8s_62179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8s_62179/02_2026/9k8s_62179.cif" } resolution = 2.9 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= 0.004 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 1200 2.51 5 N 312 2.21 5 O 366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1902 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 178 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "F" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 139 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Restraints were copied for chains: G, I, K, M, O, H, J, L, N, P Time building chain proxies: 0.39, per 1000 atoms: 0.21 Number of scatterers: 1902 At special positions: 0 Unit cell: (55.12, 100.88, 29.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 366 8.00 N 312 7.00 C 1200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.15 Conformation dependent library (CDL) restraints added in 83.2 milliseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 58 through 59 removed outlier: 6.114A pdb=" N MET E 58 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 65 through 66 removed outlier: 6.572A pdb=" N LYS E 65 " --> pdb=" O ALA I 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.116A pdb=" N MET K 58 " --> pdb=" O ALA M 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 65 through 66 removed outlier: 6.572A pdb=" N LYS K 65 " --> pdb=" O ALA O 66 " (cutoff:3.500A) 4 hydrogen bonds defined for protein. 12 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: 0.21 Time building geometry restraints manager: 0.22 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: 612 1.34 - 1.46: 227 1.46 - 1.57: 1003 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 1890 Sorted by residual: bond pdb=" CG LEU I 64 " pdb=" CD1 LEU I 64 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.22e-01 bond pdb=" CA LEU P 57 " pdb=" CB LEU P 57 " ideal model delta sigma weight residual 1.524 1.533 -0.008 1.46e-02 4.69e+03 3.12e-01 bond pdb=" CG LEU M 64 " pdb=" CD1 LEU M 64 " ideal model delta sigma weight residual 1.521 1.503 0.018 3.30e-02 9.18e+02 2.97e-01 bond pdb=" CG LEU G 64 " pdb=" CD1 LEU G 64 " ideal model delta sigma weight residual 1.521 1.503 0.018 3.30e-02 9.18e+02 2.94e-01 bond pdb=" CG LEU K 64 " pdb=" CD1 LEU K 64 " ideal model delta sigma weight residual 1.521 1.503 0.018 3.30e-02 9.18e+02 2.84e-01 ... (remaining 1885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 2374 1.50 - 3.00: 104 3.00 - 4.51: 25 4.51 - 6.01: 11 6.01 - 7.51: 6 Bond angle restraints: 2520 Sorted by residual: angle pdb=" CA LEU L 64 " pdb=" CB LEU L 64 " pdb=" CG LEU L 64 " ideal model delta sigma weight residual 116.30 123.81 -7.51 3.50e+00 8.16e-02 4.60e+00 angle pdb=" CA LEU F 64 " pdb=" CB LEU F 64 " pdb=" CG LEU F 64 " ideal model delta sigma weight residual 116.30 123.81 -7.51 3.50e+00 8.16e-02 4.60e+00 angle pdb=" CA LEU H 64 " pdb=" CB LEU H 64 " pdb=" CG LEU H 64 " ideal model delta sigma weight residual 116.30 123.80 -7.50 3.50e+00 8.16e-02 4.59e+00 angle pdb=" CA LEU P 64 " pdb=" CB LEU P 64 " pdb=" CG LEU P 64 " ideal model delta sigma weight residual 116.30 123.77 -7.47 3.50e+00 8.16e-02 4.56e+00 angle pdb=" CA LEU N 64 " pdb=" CB LEU N 64 " pdb=" CG LEU N 64 " ideal model delta sigma weight residual 116.30 123.75 -7.45 3.50e+00 8.16e-02 4.54e+00 ... (remaining 2515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 1080 15.84 - 31.69: 120 31.69 - 47.53: 30 47.53 - 63.38: 0 63.38 - 79.22: 6 Dihedral angle restraints: 1236 sinusoidal: 456 harmonic: 780 Sorted by residual: dihedral pdb=" CB GLU N 69 " pdb=" CG GLU N 69 " pdb=" CD GLU N 69 " pdb=" OE1 GLU N 69 " ideal model delta sinusoidal sigma weight residual 0.00 -79.22 79.22 1 3.00e+01 1.11e-03 8.67e+00 dihedral pdb=" CB GLU F 69 " pdb=" CG GLU F 69 " pdb=" CD GLU F 69 " pdb=" OE1 GLU F 69 " ideal model delta sinusoidal sigma weight residual 0.00 -79.22 79.22 1 3.00e+01 1.11e-03 8.67e+00 dihedral pdb=" CB GLU H 69 " pdb=" CG GLU H 69 " pdb=" CD GLU H 69 " pdb=" OE1 GLU H 69 " ideal model delta sinusoidal sigma weight residual 0.00 -79.17 79.17 1 3.00e+01 1.11e-03 8.66e+00 ... (remaining 1233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 167 0.030 - 0.060: 125 0.060 - 0.090: 43 0.090 - 0.119: 1 0.119 - 0.149: 6 Chirality restraints: 342 Sorted by residual: chirality pdb=" CA ILE E 54 " pdb=" N ILE E 54 " pdb=" C ILE E 54 " pdb=" CB ILE E 54 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ILE G 54 " pdb=" N ILE G 54 " pdb=" C ILE G 54 " pdb=" CB ILE G 54 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE M 54 " pdb=" N ILE M 54 " pdb=" C ILE M 54 " pdb=" CB ILE M 54 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 339 not shown) Planarity restraints: 300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 59 " 0.002 2.00e-02 2.50e+03 5.00e-03 2.50e-01 pdb=" C ALA G 59 " -0.009 2.00e-02 2.50e+03 pdb=" O ALA G 59 " 0.003 2.00e-02 2.50e+03 pdb=" N ASN G 60 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 59 " 0.002 2.00e-02 2.50e+03 4.78e-03 2.29e-01 pdb=" C ALA E 59 " -0.008 2.00e-02 2.50e+03 pdb=" O ALA E 59 " 0.003 2.00e-02 2.50e+03 pdb=" N ASN E 60 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 59 " -0.002 2.00e-02 2.50e+03 4.69e-03 2.20e-01 pdb=" C ALA K 59 " 0.008 2.00e-02 2.50e+03 pdb=" O ALA K 59 " -0.003 2.00e-02 2.50e+03 pdb=" N ASN K 60 " -0.003 2.00e-02 2.50e+03 ... (remaining 297 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 624 2.89 - 3.39: 1770 3.39 - 3.90: 2656 3.90 - 4.40: 2980 4.40 - 4.90: 6080 Nonbonded interactions: 14110 Sorted by model distance: nonbonded pdb=" OD1 ASN F 60 " pdb=" N ALA F 61 " model vdw 2.391 3.120 nonbonded pdb=" OD1 ASN N 60 " pdb=" N ALA N 61 " model vdw 2.392 3.120 nonbonded pdb=" OD1 ASN H 60 " pdb=" N ALA H 61 " model vdw 2.392 3.120 nonbonded pdb=" OD1 ASN P 60 " pdb=" N ALA P 61 " model vdw 2.392 3.120 nonbonded pdb=" OD1 ASN J 60 " pdb=" N ALA J 61 " model vdw 2.392 3.120 ... (remaining 14105 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: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 1.620 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 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 : 0.003 0.019 1890 Z= 0.129 Angle : 0.862 7.511 2520 Z= 0.387 Chirality : 0.044 0.149 342 Planarity : 0.001 0.005 300 Dihedral : 15.696 79.221 708 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 26.47 % Favored : 73.53 % 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: -6.41 (0.30), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.88 (0.23), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 1890) covalent geometry : angle 0.86172 ( 2520) hydrogen bonds : bond 0.08213 ( 4) hydrogen bonds : angle 7.74921 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.075 Fit side-chains REVERT: N 51 MET cc_start: 0.6084 (ttt) cc_final: 0.5727 (ttp) REVERT: N 69 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6345 (mm-30) REVERT: P 51 MET cc_start: 0.6915 (ttt) cc_final: 0.6690 (tmm) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.6250 time to fit residues: 29.2060 Evaluate side-chains 42 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 63 GLN H 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5175 r_free = 0.5175 target = 0.159192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.135841 restraints weight = 2166.530| |-----------------------------------------------------------------------------| r_work (start): 0.4992 rms_B_bonded: 3.61 r_work: 0.4862 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1890 Z= 0.113 Angle : 0.730 6.097 2520 Z= 0.331 Chirality : 0.044 0.127 342 Planarity : 0.002 0.015 300 Dihedral : 3.793 12.194 252 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.92 % Allowed : 25.49 % Favored : 70.59 % 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: -6.15 (0.30), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.23), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 1890) covalent geometry : angle 0.73035 ( 2520) hydrogen bonds : bond 0.00733 ( 4) hydrogen bonds : angle 3.90364 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.097 Fit side-chains REVERT: F 51 MET cc_start: 0.5579 (OUTLIER) cc_final: 0.5361 (tmm) REVERT: F 69 GLU cc_start: 0.6552 (mm-30) cc_final: 0.5684 (mm-30) REVERT: G 58 MET cc_start: 0.7453 (mpt) cc_final: 0.7229 (mpt) REVERT: I 58 MET cc_start: 0.6375 (mpt) cc_final: 0.6165 (mpt) REVERT: J 69 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6157 (mm-30) REVERT: L 63 GLN cc_start: 0.6572 (tm-30) cc_final: 0.6131 (tm-30) REVERT: O 46 SER cc_start: 0.8325 (t) cc_final: 0.8048 (m) REVERT: O 51 MET cc_start: 0.8240 (ppp) cc_final: 0.7943 (tmm) REVERT: P 51 MET cc_start: 0.6857 (ttt) cc_final: 0.6527 (tmm) REVERT: P 69 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6183 (pt0) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.5920 time to fit residues: 31.3113 Evaluate side-chains 43 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain M residue 46 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.146505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.122890 restraints weight = 2335.325| |-----------------------------------------------------------------------------| r_work (start): 0.4793 rms_B_bonded: 3.69 r_work: 0.4658 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1890 Z= 0.130 Angle : 0.739 6.678 2520 Z= 0.338 Chirality : 0.043 0.119 342 Planarity : 0.002 0.011 300 Dihedral : 3.938 12.593 252 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.92 % Allowed : 25.98 % Favored : 70.10 % 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: -6.06 (0.29), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.22), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 1890) covalent geometry : angle 0.73891 ( 2520) hydrogen bonds : bond 0.01185 ( 4) hydrogen bonds : angle 3.32377 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.074 Fit side-chains REVERT: E 51 MET cc_start: 0.7542 (ppp) cc_final: 0.6818 (ppp) REVERT: G 58 MET cc_start: 0.7618 (mpt) cc_final: 0.7236 (mpt) REVERT: I 44 LYS cc_start: 0.7051 (mtmt) cc_final: 0.6115 (tttt) REVERT: I 51 MET cc_start: 0.7673 (ptm) cc_final: 0.7378 (pp-130) REVERT: I 58 MET cc_start: 0.6136 (mpt) cc_final: 0.5870 (mpt) REVERT: K 51 MET cc_start: 0.7855 (ppp) cc_final: 0.7171 (ppp) REVERT: K 52 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6922 (tt) REVERT: L 63 GLN cc_start: 0.6231 (tm-30) cc_final: 0.5876 (tm-30) REVERT: M 58 MET cc_start: 0.8014 (mtp) cc_final: 0.7139 (mpt) REVERT: O 51 MET cc_start: 0.8264 (ppp) cc_final: 0.7723 (tmm) REVERT: P 51 MET cc_start: 0.6841 (ttt) cc_final: 0.6525 (tmm) REVERT: P 69 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6253 (pp20) outliers start: 8 outliers final: 2 residues processed: 49 average time/residue: 0.5975 time to fit residues: 29.7380 Evaluate side-chains 43 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain M residue 46 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.0050 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.145907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.121573 restraints weight = 2263.653| |-----------------------------------------------------------------------------| r_work (start): 0.4780 rms_B_bonded: 3.70 r_work: 0.4638 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1890 Z= 0.153 Angle : 0.731 5.492 2520 Z= 0.332 Chirality : 0.043 0.124 342 Planarity : 0.002 0.011 300 Dihedral : 4.077 14.246 252 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.39 % Allowed : 25.49 % Favored : 69.12 % 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: -6.09 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.20), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 1890) covalent geometry : angle 0.73077 ( 2520) hydrogen bonds : bond 0.01515 ( 4) hydrogen bonds : angle 3.11529 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.076 Fit side-chains REVERT: E 51 MET cc_start: 0.7413 (ppp) cc_final: 0.7187 (ppp) REVERT: F 51 MET cc_start: 0.5466 (tmm) cc_final: 0.5257 (tmm) REVERT: G 51 MET cc_start: 0.8025 (pp-130) cc_final: 0.7758 (pp-130) REVERT: G 58 MET cc_start: 0.7727 (mpt) cc_final: 0.7438 (mpt) REVERT: I 44 LYS cc_start: 0.7101 (mtmt) cc_final: 0.6020 (tttt) REVERT: I 58 MET cc_start: 0.6329 (mpt) cc_final: 0.6054 (mpt) REVERT: I 60 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.6966 (p0) REVERT: K 51 MET cc_start: 0.7823 (ppp) cc_final: 0.7351 (ppp) REVERT: M 51 MET cc_start: 0.7958 (ppp) cc_final: 0.5212 (tpt) REVERT: M 58 MET cc_start: 0.8093 (mtp) cc_final: 0.7107 (mpt) REVERT: O 51 MET cc_start: 0.8172 (ppp) cc_final: 0.7617 (tmm) REVERT: P 51 MET cc_start: 0.6799 (ttt) cc_final: 0.6467 (tmm) REVERT: P 69 GLU cc_start: 0.6621 (mm-30) cc_final: 0.5801 (pm20) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.6271 time to fit residues: 33.1079 Evaluate side-chains 46 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain O residue 50 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN L 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.162228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.135963 restraints weight = 2133.904| |-----------------------------------------------------------------------------| r_work (start): 0.4855 rms_B_bonded: 3.87 r_work: 0.4711 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1890 Z= 0.121 Angle : 0.684 5.590 2520 Z= 0.309 Chirality : 0.041 0.125 342 Planarity : 0.001 0.007 300 Dihedral : 3.825 14.435 252 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 3.43 % Allowed : 26.47 % Favored : 70.10 % 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: -5.93 (0.28), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.21), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 1890) covalent geometry : angle 0.68436 ( 2520) hydrogen bonds : bond 0.01006 ( 4) hydrogen bonds : angle 3.22425 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.076 Fit side-chains REVERT: E 51 MET cc_start: 0.7582 (ppp) cc_final: 0.6910 (ppp) REVERT: E 56 LEU cc_start: 0.6954 (mp) cc_final: 0.6604 (tt) REVERT: F 51 MET cc_start: 0.5459 (tmm) cc_final: 0.4995 (tmm) REVERT: G 51 MET cc_start: 0.7706 (pp-130) cc_final: 0.7490 (pp-130) REVERT: G 58 MET cc_start: 0.7687 (mpt) cc_final: 0.7370 (mpt) REVERT: H 51 MET cc_start: 0.5669 (OUTLIER) cc_final: 0.4930 (tmm) REVERT: I 44 LYS cc_start: 0.6982 (mtmt) cc_final: 0.5914 (tttt) REVERT: K 51 MET cc_start: 0.7878 (ppp) cc_final: 0.7050 (ppp) REVERT: K 53 ASP cc_start: 0.7540 (t0) cc_final: 0.7337 (t0) REVERT: M 45 LYS cc_start: 0.8464 (mtmt) cc_final: 0.7837 (ptpp) REVERT: M 58 MET cc_start: 0.7985 (mtp) cc_final: 0.7121 (mpt) REVERT: O 51 MET cc_start: 0.8169 (ppp) cc_final: 0.7545 (tmm) REVERT: P 51 MET cc_start: 0.6760 (ttt) cc_final: 0.6414 (tmm) REVERT: P 69 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6260 (pp20) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 0.5940 time to fit residues: 28.3725 Evaluate side-chains 46 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain O residue 50 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN L 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.154700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.128312 restraints weight = 2254.283| |-----------------------------------------------------------------------------| r_work (start): 0.4779 rms_B_bonded: 3.62 r_work: 0.4636 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1890 Z= 0.181 Angle : 0.728 5.890 2520 Z= 0.335 Chirality : 0.041 0.113 342 Planarity : 0.002 0.008 300 Dihedral : 4.214 13.708 252 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.86 % Allowed : 25.98 % Favored : 67.16 % 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: -6.03 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.21), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 1890) covalent geometry : angle 0.72786 ( 2520) hydrogen bonds : bond 0.01763 ( 4) hydrogen bonds : angle 3.28728 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.076 Fit side-chains REVERT: E 51 MET cc_start: 0.7428 (ppp) cc_final: 0.7225 (ptt) REVERT: E 52 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6800 (tt) REVERT: G 51 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7783 (pp-130) REVERT: G 58 MET cc_start: 0.7686 (mpt) cc_final: 0.7340 (mpt) REVERT: I 44 LYS cc_start: 0.7103 (mtmt) cc_final: 0.5984 (tttt) REVERT: I 51 MET cc_start: 0.7686 (ptm) cc_final: 0.7468 (ptt) REVERT: I 58 MET cc_start: 0.6619 (mpt) cc_final: 0.6354 (mpt) REVERT: I 60 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7028 (p0) REVERT: J 69 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6433 (tm-30) REVERT: K 51 MET cc_start: 0.7886 (ppp) cc_final: 0.7452 (ppp) REVERT: M 51 MET cc_start: 0.7847 (ppp) cc_final: 0.5085 (tpt) REVERT: M 58 MET cc_start: 0.8070 (mtp) cc_final: 0.7077 (mpt) REVERT: O 51 MET cc_start: 0.8042 (ppp) cc_final: 0.7492 (tmm) REVERT: P 51 MET cc_start: 0.6798 (ttt) cc_final: 0.6477 (tmm) REVERT: P 69 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6126 (pt0) outliers start: 14 outliers final: 5 residues processed: 49 average time/residue: 0.5976 time to fit residues: 29.7534 Evaluate side-chains 47 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain O residue 50 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN L 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.151475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.125505 restraints weight = 2190.011| |-----------------------------------------------------------------------------| r_work (start): 0.4819 rms_B_bonded: 3.71 r_work: 0.4682 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1890 Z= 0.110 Angle : 0.671 7.290 2520 Z= 0.301 Chirality : 0.041 0.117 342 Planarity : 0.001 0.014 300 Dihedral : 3.678 13.778 252 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.43 % Allowed : 30.39 % Favored : 66.18 % 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: -5.88 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.21), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 1890) covalent geometry : angle 0.67109 ( 2520) hydrogen bonds : bond 0.01027 ( 4) hydrogen bonds : angle 3.49193 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.043 Fit side-chains REVERT: E 51 MET cc_start: 0.7344 (ppp) cc_final: 0.7055 (ptt) REVERT: E 56 LEU cc_start: 0.7190 (mp) cc_final: 0.6821 (tt) REVERT: F 51 MET cc_start: 0.5558 (tmm) cc_final: 0.5115 (tmm) REVERT: G 51 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7358 (pp-130) REVERT: G 58 MET cc_start: 0.7489 (mpt) cc_final: 0.7186 (mpt) REVERT: H 51 MET cc_start: 0.5758 (OUTLIER) cc_final: 0.5031 (tmt) REVERT: I 44 LYS cc_start: 0.7175 (mtmt) cc_final: 0.6052 (tttt) REVERT: I 51 MET cc_start: 0.7711 (ptm) cc_final: 0.7489 (ptt) REVERT: I 58 MET cc_start: 0.6479 (mpt) cc_final: 0.6209 (mpt) REVERT: K 51 MET cc_start: 0.7890 (ppp) cc_final: 0.7315 (ppp) REVERT: L 63 GLN cc_start: 0.7018 (tt0) cc_final: 0.6817 (tt0) REVERT: M 51 MET cc_start: 0.7796 (ppp) cc_final: 0.4833 (tpt) REVERT: M 58 MET cc_start: 0.7941 (mtp) cc_final: 0.7045 (mpt) REVERT: O 51 MET cc_start: 0.8020 (ppp) cc_final: 0.7445 (tmm) REVERT: P 51 MET cc_start: 0.6851 (ttt) cc_final: 0.6507 (tmm) REVERT: P 69 GLU cc_start: 0.6452 (mm-30) cc_final: 0.6252 (pp20) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.4508 time to fit residues: 21.0416 Evaluate side-chains 47 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain O residue 50 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.0010 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 63 GLN ** 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 = 0.5232 r_free = 0.5232 target = 0.164525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.139484 restraints weight = 2249.581| |-----------------------------------------------------------------------------| r_work (start): 0.4967 rms_B_bonded: 3.75 r_work: 0.4849 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1890 Z= 0.111 Angle : 0.678 7.279 2520 Z= 0.303 Chirality : 0.041 0.127 342 Planarity : 0.001 0.007 300 Dihedral : 3.632 14.366 252 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 29.41 % Favored : 66.67 % 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: -5.70 (0.28), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.21), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 1890) covalent geometry : angle 0.67806 ( 2520) hydrogen bonds : bond 0.01007 ( 4) hydrogen bonds : angle 3.28391 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.045 Fit side-chains REVERT: E 51 MET cc_start: 0.7484 (ppp) cc_final: 0.6894 (ppp) REVERT: E 52 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6902 (tt) REVERT: G 58 MET cc_start: 0.7465 (mpt) cc_final: 0.7172 (mpt) REVERT: G 63 GLN cc_start: 0.7585 (mt0) cc_final: 0.7200 (mt0) REVERT: H 51 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.5184 (tmt) REVERT: I 44 LYS cc_start: 0.7346 (mtmt) cc_final: 0.6304 (tttt) REVERT: I 51 MET cc_start: 0.7566 (ptm) cc_final: 0.7137 (ptt) REVERT: I 58 MET cc_start: 0.6670 (mpt) cc_final: 0.6383 (mpt) REVERT: K 51 MET cc_start: 0.7776 (ppp) cc_final: 0.7492 (ppp) REVERT: L 63 GLN cc_start: 0.7284 (tt0) cc_final: 0.7074 (tt0) REVERT: M 45 LYS cc_start: 0.8514 (mtmt) cc_final: 0.7896 (ptpt) REVERT: M 51 MET cc_start: 0.7700 (ppp) cc_final: 0.4735 (tpt) REVERT: M 58 MET cc_start: 0.7848 (mtp) cc_final: 0.7115 (mpt) REVERT: O 51 MET cc_start: 0.7914 (ppp) cc_final: 0.7538 (tmm) REVERT: O 52 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6660 (tt) REVERT: P 51 MET cc_start: 0.6818 (ttt) cc_final: 0.6477 (tmm) REVERT: P 58 MET cc_start: 0.6101 (ppp) cc_final: 0.5900 (ptm) REVERT: P 69 GLU cc_start: 0.6567 (mm-30) cc_final: 0.6325 (pp20) outliers start: 8 outliers final: 2 residues processed: 48 average time/residue: 0.4362 time to fit residues: 21.2548 Evaluate side-chains 47 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain O residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 63 GLN ** 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 = 0.5206 r_free = 0.5206 target = 0.161643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.136458 restraints weight = 2274.990| |-----------------------------------------------------------------------------| r_work (start): 0.4944 rms_B_bonded: 3.74 r_work: 0.4820 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1890 Z= 0.135 Angle : 0.745 7.079 2520 Z= 0.332 Chirality : 0.041 0.127 342 Planarity : 0.001 0.007 300 Dihedral : 3.776 14.947 252 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.92 % Allowed : 30.39 % Favored : 65.69 % 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: -5.65 (0.28), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.21), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 1890) covalent geometry : angle 0.74489 ( 2520) hydrogen bonds : bond 0.01764 ( 4) hydrogen bonds : angle 3.10277 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.097 Fit side-chains REVERT: E 56 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6387 (tt) REVERT: G 58 MET cc_start: 0.7473 (mpt) cc_final: 0.7159 (mpt) REVERT: H 51 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5221 (tmt) REVERT: I 44 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6146 (tttt) REVERT: I 51 MET cc_start: 0.7612 (ptm) cc_final: 0.7398 (ptt) REVERT: I 58 MET cc_start: 0.6707 (mpt) cc_final: 0.6409 (mpt) REVERT: J 69 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6678 (tm-30) REVERT: K 51 MET cc_start: 0.7815 (ppp) cc_final: 0.7512 (ppp) REVERT: M 51 MET cc_start: 0.7846 (ppp) cc_final: 0.4828 (tpt) REVERT: M 58 MET cc_start: 0.7867 (mtp) cc_final: 0.7042 (mpt) REVERT: O 51 MET cc_start: 0.7933 (ppp) cc_final: 0.7542 (tmm) REVERT: P 51 MET cc_start: 0.6830 (ttt) cc_final: 0.6495 (tmm) REVERT: P 58 MET cc_start: 0.6282 (ppp) cc_final: 0.6043 (ptm) REVERT: P 69 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6172 (pt0) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.5329 time to fit residues: 25.4354 Evaluate side-chains 50 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain O residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 63 GLN L 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.153077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.126700 restraints weight = 2364.602| |-----------------------------------------------------------------------------| r_work (start): 0.4847 rms_B_bonded: 3.97 r_work: 0.4722 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 1890 Z= 0.202 Angle : 0.852 7.657 2520 Z= 0.387 Chirality : 0.042 0.133 342 Planarity : 0.002 0.017 300 Dihedral : 4.463 18.590 252 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.43 % Allowed : 30.88 % Favored : 65.69 % 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: -5.81 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.21), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 1890) covalent geometry : angle 0.85223 ( 2520) hydrogen bonds : bond 0.02612 ( 4) hydrogen bonds : angle 3.11726 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.049 Fit side-chains REVERT: E 52 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6749 (tt) REVERT: F 58 MET cc_start: 0.6013 (tpp) cc_final: 0.5753 (tpp) REVERT: G 58 MET cc_start: 0.7624 (mpt) cc_final: 0.7300 (mpt) REVERT: H 51 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.4695 (tmt) REVERT: I 44 LYS cc_start: 0.6987 (mtmt) cc_final: 0.5864 (tttt) REVERT: I 51 MET cc_start: 0.7609 (ptm) cc_final: 0.6954 (ptt) REVERT: I 58 MET cc_start: 0.6662 (mpt) cc_final: 0.6324 (mpt) REVERT: J 62 SER cc_start: 0.7270 (t) cc_final: 0.6966 (p) REVERT: J 69 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6689 (tm-30) REVERT: K 51 MET cc_start: 0.7728 (ppp) cc_final: 0.6976 (ppp) REVERT: L 69 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6450 (tm-30) REVERT: M 51 MET cc_start: 0.7905 (ppp) cc_final: 0.7592 (ppp) REVERT: M 58 MET cc_start: 0.8202 (mtp) cc_final: 0.7051 (mpt) REVERT: O 51 MET cc_start: 0.7998 (ppp) cc_final: 0.7336 (tmm) REVERT: O 63 GLN cc_start: 0.8253 (mt0) cc_final: 0.7855 (mp10) REVERT: P 51 MET cc_start: 0.6736 (ttt) cc_final: 0.6402 (tmm) REVERT: P 69 GLU cc_start: 0.6453 (mm-30) cc_final: 0.6045 (pt0) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.4116 time to fit residues: 20.9077 Evaluate side-chains 51 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain O residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.164137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.136511 restraints weight = 2269.795| |-----------------------------------------------------------------------------| r_work (start): 0.4950 rms_B_bonded: 4.11 r_work: 0.4820 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1890 Z= 0.116 Angle : 0.782 8.092 2520 Z= 0.348 Chirality : 0.041 0.126 342 Planarity : 0.002 0.019 300 Dihedral : 3.808 15.379 252 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 30.39 % Favored : 65.69 % 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: -5.52 (0.29), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.22), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 1890) covalent geometry : angle 0.78150 ( 2520) hydrogen bonds : bond 0.00952 ( 4) hydrogen bonds : angle 3.69100 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 860.84 seconds wall clock time: 15 minutes 21.18 seconds (921.18 seconds total)