Starting phenix.real_space_refine on Tue Mar 3 10:47:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g2v_29682/03_2026/8g2v_29682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g2v_29682/03_2026/8g2v_29682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.715 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g2v_29682/03_2026/8g2v_29682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g2v_29682/03_2026/8g2v_29682.map" model { file = "/net/cci-nas-00/data/ceres_data/8g2v_29682/03_2026/8g2v_29682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g2v_29682/03_2026/8g2v_29682.cif" } resolution = 2.715 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= 0.003 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 10 5.16 5 C 1030 2.51 5 N 320 2.21 5 O 300 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1660 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.18, per 1000 atoms: 0.11 Number of scatterers: 1660 At special positions: 0 Unit cell: (61.523, 55.131, 39.151, 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 10 16.00 O 300 8.00 N 320 7.00 C 1030 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: 0.06 Conformation dependent library (CDL) restraints added in 34.1 milliseconds 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 380 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.890A pdb=" N GLY D 58 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY A 58 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY E 58 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY I 58 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU I 60 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 67 through 70 removed outlier: 6.284A pdb=" N ASN A 67 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASN E 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE A 69 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN E 67 " --> pdb=" O ALA I 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 73 through 74 removed outlier: 6.412A pdb=" N VAL A 73 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL E 73 " --> pdb=" O ARG I 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 57 through 60 removed outlier: 6.389A pdb=" N GLY B 58 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY C 58 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY G 58 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY J 58 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 67 through 70 removed outlier: 6.283A pdb=" N ASN B 67 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASN C 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 69 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN C 67 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASN G 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE C 69 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASN G 67 " --> pdb=" O ALA J 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 73 through 74 removed outlier: 6.409A pdb=" N VAL B 73 " --> pdb=" O ARG C 74 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL C 73 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL G 73 " --> pdb=" O ARG J 74 " (cutoff:3.500A) 23 hydrogen bonds defined for protein. 69 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: 0.11 Time building geometry restraints manager: 0.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 580 1.34 - 1.46: 151 1.46 - 1.57: 919 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 1670 Sorted by residual: bond pdb=" N GLU I 60 " pdb=" CA GLU I 60 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.19e-02 7.06e+03 4.82e+00 bond pdb=" N GLU B 60 " pdb=" CA GLU B 60 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.19e-02 7.06e+03 4.74e+00 bond pdb=" N GLU A 60 " pdb=" CA GLU A 60 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.19e-02 7.06e+03 4.67e+00 bond pdb=" N GLU D 60 " pdb=" CA GLU D 60 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.19e-02 7.06e+03 4.63e+00 bond pdb=" N GLU E 60 " pdb=" CA GLU E 60 " ideal model delta sigma weight residual 1.458 1.483 -0.026 1.19e-02 7.06e+03 4.60e+00 ... (remaining 1665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 1930 0.87 - 1.75: 260 1.75 - 2.62: 30 2.62 - 3.50: 0 3.50 - 4.37: 10 Bond angle restraints: 2230 Sorted by residual: angle pdb=" CA ASN E 70 " pdb=" C ASN E 70 " pdb=" O ASN E 70 " ideal model delta sigma weight residual 120.58 118.51 2.07 1.07e+00 8.73e-01 3.74e+00 angle pdb=" CA ASN H 70 " pdb=" C ASN H 70 " pdb=" O ASN H 70 " ideal model delta sigma weight residual 120.58 118.55 2.03 1.07e+00 8.73e-01 3.60e+00 angle pdb=" CA ASN D 70 " pdb=" C ASN D 70 " pdb=" O ASN D 70 " ideal model delta sigma weight residual 120.58 118.55 2.03 1.07e+00 8.73e-01 3.59e+00 angle pdb=" CA ASN A 70 " pdb=" C ASN A 70 " pdb=" O ASN A 70 " ideal model delta sigma weight residual 120.58 118.56 2.02 1.07e+00 8.73e-01 3.57e+00 angle pdb=" CA ASN F 70 " pdb=" C ASN F 70 " pdb=" O ASN F 70 " ideal model delta sigma weight residual 120.58 118.59 1.99 1.07e+00 8.73e-01 3.47e+00 ... (remaining 2225 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.40: 940 13.40 - 26.79: 70 26.79 - 40.18: 0 40.18 - 53.57: 20 53.57 - 66.96: 20 Dihedral angle restraints: 1050 sinusoidal: 460 harmonic: 590 Sorted by residual: dihedral pdb=" CA GLU I 60 " pdb=" CB GLU I 60 " pdb=" CG GLU I 60 " pdb=" CD GLU I 60 " ideal model delta sinusoidal sigma weight residual 180.00 -131.06 -48.94 3 1.50e+01 4.44e-03 8.71e+00 dihedral pdb=" CA GLU G 60 " pdb=" CB GLU G 60 " pdb=" CG GLU G 60 " pdb=" CD GLU G 60 " ideal model delta sinusoidal sigma weight residual 180.00 -131.10 -48.90 3 1.50e+01 4.44e-03 8.70e+00 dihedral pdb=" CA GLU A 60 " pdb=" CB GLU A 60 " pdb=" CG GLU A 60 " pdb=" CD GLU A 60 " ideal model delta sinusoidal sigma weight residual -180.00 -131.12 -48.88 3 1.50e+01 4.44e-03 8.70e+00 ... (remaining 1047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.031: 114 0.031 - 0.060: 53 0.060 - 0.090: 23 0.090 - 0.119: 40 0.119 - 0.148: 10 Chirality restraints: 240 Sorted by residual: chirality pdb=" CA GLU A 60 " pdb=" N GLU A 60 " pdb=" C GLU A 60 " pdb=" CB GLU A 60 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA GLU E 60 " pdb=" N GLU E 60 " pdb=" C GLU E 60 " pdb=" CB GLU E 60 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA GLU H 60 " pdb=" N GLU H 60 " pdb=" C GLU H 60 " pdb=" CB GLU H 60 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 237 not shown) Planarity restraints: 300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 59 " -0.004 2.00e-02 2.50e+03 8.82e-03 7.78e-01 pdb=" C GLN D 59 " 0.015 2.00e-02 2.50e+03 pdb=" O GLN D 59 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU D 60 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 59 " -0.004 2.00e-02 2.50e+03 8.81e-03 7.77e-01 pdb=" C GLN E 59 " 0.015 2.00e-02 2.50e+03 pdb=" O GLN E 59 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU E 60 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 59 " 0.004 2.00e-02 2.50e+03 8.79e-03 7.72e-01 pdb=" C GLN F 59 " -0.015 2.00e-02 2.50e+03 pdb=" O GLN F 59 " 0.006 2.00e-02 2.50e+03 pdb=" N GLU F 60 " 0.005 2.00e-02 2.50e+03 ... (remaining 297 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 799 2.97 - 3.45: 1533 3.45 - 3.93: 2787 3.93 - 4.42: 2944 4.42 - 4.90: 5645 Nonbonded interactions: 13708 Sorted by model distance: nonbonded pdb=" N LYS A 61 " pdb=" O GLU E 60 " model vdw 2.486 3.120 nonbonded pdb=" N LYS C 61 " pdb=" O GLU G 60 " model vdw 2.492 3.120 nonbonded pdb=" O GLU B 60 " pdb=" N LYS F 61 " model vdw 2.492 3.120 nonbonded pdb=" N LYS B 61 " pdb=" O GLU C 60 " model vdw 2.492 3.120 nonbonded pdb=" O GLU A 60 " pdb=" N LYS D 61 " model vdw 2.498 3.120 ... (remaining 13703 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.530 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.070 Find NCS groups from input model: 0.010 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:4.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.005 0.031 1670 Z= 0.309 Angle : 0.637 4.375 2230 Z= 0.408 Chirality : 0.063 0.148 240 Planarity : 0.004 0.017 300 Dihedral : 16.255 66.959 670 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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: -3.75 (0.39), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.29), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 74 TYR 0.005 0.001 TYR C 63 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 1670) covalent geometry : angle 0.63731 ( 2230) hydrogen bonds : bond 0.20209 ( 23) hydrogen bonds : angle 7.69387 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.053 Fit side-chains REVERT: B 64 GLN cc_start: 0.8667 (mt0) cc_final: 0.8403 (mt0) REVERT: J 74 ARG cc_start: 0.6515 (ttt-90) cc_final: 0.6254 (tpm170) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3652 time to fit residues: 19.2689 Evaluate side-chains 48 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.183983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.170098 restraints weight = 1671.063| |-----------------------------------------------------------------------------| r_work (start): 0.4815 rms_B_bonded: 1.92 r_work: 0.4722 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4596 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1670 Z= 0.114 Angle : 0.559 4.192 2230 Z= 0.302 Chirality : 0.057 0.131 240 Planarity : 0.003 0.019 300 Dihedral : 5.015 11.749 220 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 7.78 % Allowed : 11.11 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.63 (0.44), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 74 TYR 0.009 0.001 TYR B 63 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 1670) covalent geometry : angle 0.55887 ( 2230) hydrogen bonds : bond 0.02177 ( 23) hydrogen bonds : angle 6.00530 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.072 Fit side-chains REVERT: B 60 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: D 55 MET cc_start: 0.5250 (OUTLIER) cc_final: 0.3857 (tmt) REVERT: D 60 GLU cc_start: 0.7694 (mp0) cc_final: 0.7059 (mp0) REVERT: F 55 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.4477 (tmt) REVERT: G 55 MET cc_start: 0.5053 (OUTLIER) cc_final: 0.4306 (tmt) REVERT: H 55 MET cc_start: 0.5890 (OUTLIER) cc_final: 0.4546 (tmt) REVERT: I 74 ARG cc_start: 0.6382 (ttt-90) cc_final: 0.5342 (tpm170) REVERT: J 66 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7407 (mtmt) REVERT: J 74 ARG cc_start: 0.6826 (ttt-90) cc_final: 0.5914 (tpm170) outliers start: 14 outliers final: 2 residues processed: 63 average time/residue: 0.4523 time to fit residues: 28.9184 Evaluate side-chains 60 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain G residue 55 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.0020 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 2 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN G 64 GLN H 64 GLN H 67 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.182000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.168726 restraints weight = 1687.494| |-----------------------------------------------------------------------------| r_work (start): 0.4781 rms_B_bonded: 1.92 r_work: 0.4678 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4556 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1670 Z= 0.106 Angle : 0.549 3.836 2230 Z= 0.298 Chirality : 0.059 0.140 240 Planarity : 0.003 0.027 300 Dihedral : 4.844 11.915 220 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.56 % Allowed : 15.56 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.59 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.35), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 74 TYR 0.008 0.001 TYR D 63 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 1670) covalent geometry : angle 0.54890 ( 2230) hydrogen bonds : bond 0.02123 ( 23) hydrogen bonds : angle 5.38998 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.071 Fit side-chains REVERT: B 60 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: I 74 ARG cc_start: 0.6767 (ttt-90) cc_final: 0.5809 (tpm170) REVERT: J 60 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7920 (mm-30) REVERT: J 66 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7483 (mtmt) REVERT: J 74 ARG cc_start: 0.7037 (ttt-90) cc_final: 0.6085 (tpm170) outliers start: 10 outliers final: 3 residues processed: 56 average time/residue: 0.6579 time to fit residues: 37.3375 Evaluate side-chains 51 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.0010 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.0470 chunk 17 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN G 64 GLN H 64 GLN H 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.185407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.170142 restraints weight = 1614.252| |-----------------------------------------------------------------------------| r_work (start): 0.4801 rms_B_bonded: 2.03 r_work: 0.4700 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4572 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1670 Z= 0.094 Angle : 0.517 3.647 2230 Z= 0.282 Chirality : 0.059 0.134 240 Planarity : 0.003 0.021 300 Dihedral : 4.648 12.931 220 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.44 % Allowed : 18.89 % Favored : 76.67 % 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: -3.58 (0.48), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 74 TYR 0.006 0.001 TYR D 63 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 1670) covalent geometry : angle 0.51682 ( 2230) hydrogen bonds : bond 0.01817 ( 23) hydrogen bonds : angle 5.23593 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.080 Fit side-chains REVERT: C 60 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7716 (mm-30) REVERT: G 60 GLU cc_start: 0.7954 (mp0) cc_final: 0.7580 (mm-30) REVERT: I 66 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7539 (mtmt) REVERT: I 74 ARG cc_start: 0.6947 (ttt-90) cc_final: 0.6622 (ttt90) REVERT: J 60 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7916 (mm-30) REVERT: J 66 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7508 (mtmt) REVERT: J 74 ARG cc_start: 0.7042 (ttt-90) cc_final: 0.5991 (tpm170) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 0.6725 time to fit residues: 36.1246 Evaluate side-chains 51 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN F 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.164941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.149457 restraints weight = 1711.442| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 2.22 r_work: 0.4449 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4317 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1670 Z= 0.188 Angle : 0.607 5.396 2230 Z= 0.329 Chirality : 0.059 0.159 240 Planarity : 0.003 0.025 300 Dihedral : 5.039 13.590 220 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 6.11 % Allowed : 16.11 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.48 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 74 TYR 0.012 0.002 TYR D 63 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 1670) covalent geometry : angle 0.60748 ( 2230) hydrogen bonds : bond 0.01641 ( 23) hydrogen bonds : angle 5.00695 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.070 Fit side-chains REVERT: C 60 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7308 (mm-30) REVERT: F 55 MET cc_start: 0.5863 (OUTLIER) cc_final: 0.4746 (tmt) REVERT: G 60 GLU cc_start: 0.7935 (mp0) cc_final: 0.6463 (mp0) REVERT: H 55 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.4652 (tmt) REVERT: H 64 GLN cc_start: 0.8609 (mt0) cc_final: 0.8393 (mt0) REVERT: I 66 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7568 (mtmt) REVERT: J 60 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8270 (mm-30) outliers start: 11 outliers final: 2 residues processed: 60 average time/residue: 0.6184 time to fit residues: 37.6350 Evaluate side-chains 53 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain J residue 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN H 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.166082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.151262 restraints weight = 1706.255| |-----------------------------------------------------------------------------| r_work (start): 0.4587 rms_B_bonded: 2.15 r_work: 0.4473 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4345 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1670 Z= 0.150 Angle : 0.583 4.290 2230 Z= 0.317 Chirality : 0.060 0.151 240 Planarity : 0.003 0.017 300 Dihedral : 4.933 13.442 220 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 6.67 % Allowed : 18.89 % Favored : 74.44 % 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: -3.47 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 74 TYR 0.012 0.002 TYR D 63 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 1670) covalent geometry : angle 0.58317 ( 2230) hydrogen bonds : bond 0.01522 ( 23) hydrogen bonds : angle 5.08073 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.092 Fit side-chains REVERT: C 60 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7348 (mm-30) REVERT: D 55 MET cc_start: 0.5077 (OUTLIER) cc_final: 0.4148 (tmt) REVERT: G 60 GLU cc_start: 0.7937 (mp0) cc_final: 0.6368 (mp0) REVERT: H 55 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.4607 (tmt) REVERT: J 60 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8212 (mm-30) REVERT: J 66 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7602 (mtmt) outliers start: 12 outliers final: 3 residues processed: 52 average time/residue: 0.6269 time to fit residues: 33.1296 Evaluate side-chains 49 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 0.0020 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 2 optimal weight: 0.0470 chunk 12 optimal weight: 0.6980 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.173271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.158196 restraints weight = 1669.359| |-----------------------------------------------------------------------------| r_work (start): 0.4678 rms_B_bonded: 2.15 r_work: 0.4562 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4435 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1670 Z= 0.107 Angle : 0.576 4.716 2230 Z= 0.313 Chirality : 0.060 0.146 240 Planarity : 0.002 0.014 300 Dihedral : 4.765 12.685 220 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.89 % Allowed : 21.67 % Favored : 74.44 % 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: -3.42 (0.49), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 74 TYR 0.018 0.002 TYR I 63 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 1670) covalent geometry : angle 0.57598 ( 2230) hydrogen bonds : bond 0.01668 ( 23) hydrogen bonds : angle 5.01159 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.044 Fit side-chains REVERT: C 60 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7555 (mm-30) REVERT: D 55 MET cc_start: 0.5007 (OUTLIER) cc_final: 0.4379 (tmm) REVERT: F 55 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.4668 (tmt) REVERT: G 60 GLU cc_start: 0.7928 (mp0) cc_final: 0.6395 (mp0) REVERT: H 55 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.4581 (tmt) REVERT: I 74 ARG cc_start: 0.7302 (ttt-90) cc_final: 0.6192 (tpm170) REVERT: J 60 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8114 (mm-30) REVERT: J 66 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7623 (mtmt) outliers start: 7 outliers final: 2 residues processed: 50 average time/residue: 0.6343 time to fit residues: 32.1328 Evaluate side-chains 52 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.0000 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN H 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.170737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.155886 restraints weight = 1685.246| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 2.15 r_work: 0.4531 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4405 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1670 Z= 0.134 Angle : 0.585 4.885 2230 Z= 0.317 Chirality : 0.060 0.141 240 Planarity : 0.002 0.014 300 Dihedral : 4.839 12.858 220 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.00 % Allowed : 20.56 % Favored : 74.44 % 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: -3.26 (0.50), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 74 TYR 0.008 0.001 TYR D 63 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 1670) covalent geometry : angle 0.58483 ( 2230) hydrogen bonds : bond 0.01571 ( 23) hydrogen bonds : angle 4.96262 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.045 Fit side-chains REVERT: C 60 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7625 (mm-30) REVERT: D 55 MET cc_start: 0.4988 (OUTLIER) cc_final: 0.4393 (tmm) REVERT: F 55 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.4795 (tmt) REVERT: G 60 GLU cc_start: 0.7952 (mp0) cc_final: 0.6374 (mp0) REVERT: H 55 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.4564 (tmt) REVERT: H 64 GLN cc_start: 0.8620 (mt0) cc_final: 0.8375 (mt0) REVERT: I 55 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.4594 (tmt) REVERT: J 60 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8104 (mm-30) REVERT: J 66 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7589 (mtmt) outliers start: 9 outliers final: 1 residues processed: 50 average time/residue: 0.5982 time to fit residues: 30.3278 Evaluate side-chains 51 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.168866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.154032 restraints weight = 1702.111| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 2.17 r_work: 0.4509 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4386 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1670 Z= 0.141 Angle : 0.590 5.872 2230 Z= 0.322 Chirality : 0.061 0.143 240 Planarity : 0.002 0.014 300 Dihedral : 4.887 12.777 220 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.33 % Allowed : 23.33 % Favored : 73.33 % 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: -3.17 (0.50), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 74 TYR 0.020 0.002 TYR I 63 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 1670) covalent geometry : angle 0.59014 ( 2230) hydrogen bonds : bond 0.01606 ( 23) hydrogen bonds : angle 5.00302 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.076 Fit side-chains REVERT: C 60 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7612 (mm-30) REVERT: D 55 MET cc_start: 0.5074 (OUTLIER) cc_final: 0.4484 (tmm) REVERT: F 55 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.4751 (tmt) REVERT: G 60 GLU cc_start: 0.7961 (mp0) cc_final: 0.6378 (mp0) REVERT: H 55 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.4515 (tmt) REVERT: J 60 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8142 (mm-30) REVERT: J 66 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7571 (mtmt) outliers start: 6 outliers final: 1 residues processed: 48 average time/residue: 0.5671 time to fit residues: 27.6117 Evaluate side-chains 49 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.0370 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.170108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.155384 restraints weight = 1708.652| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 2.17 r_work: 0.4537 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4410 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1670 Z= 0.126 Angle : 0.601 5.679 2230 Z= 0.328 Chirality : 0.061 0.146 240 Planarity : 0.002 0.013 300 Dihedral : 4.877 13.137 220 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.78 % Allowed : 24.44 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.12 (0.51), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 74 TYR 0.009 0.001 TYR D 63 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 1670) covalent geometry : angle 0.60093 ( 2230) hydrogen bonds : bond 0.01582 ( 23) hydrogen bonds : angle 4.97531 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.074 Fit side-chains REVERT: C 60 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7648 (mm-30) REVERT: D 55 MET cc_start: 0.5039 (OUTLIER) cc_final: 0.4468 (tmm) REVERT: F 55 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.4794 (tmt) REVERT: G 60 GLU cc_start: 0.7987 (mp0) cc_final: 0.6381 (mp0) REVERT: H 55 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.4547 (tmt) REVERT: J 60 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8092 (mm-30) REVERT: J 66 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7551 (mtmt) outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 0.5812 time to fit residues: 27.7261 Evaluate side-chains 48 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.170861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.156244 restraints weight = 1669.092| |-----------------------------------------------------------------------------| r_work (start): 0.4654 rms_B_bonded: 2.13 r_work: 0.4547 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4424 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1670 Z= 0.124 Angle : 0.590 5.671 2230 Z= 0.322 Chirality : 0.060 0.145 240 Planarity : 0.002 0.013 300 Dihedral : 4.797 12.725 220 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.33 % Allowed : 23.89 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.08 (0.52), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 74 TYR 0.009 0.001 TYR D 63 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 1670) covalent geometry : angle 0.59021 ( 2230) hydrogen bonds : bond 0.01638 ( 23) hydrogen bonds : angle 4.91894 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1165.69 seconds wall clock time: 20 minutes 31.25 seconds (1231.25 seconds total)