Starting phenix.real_space_refine on Mon Feb 10 19:40:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g2v_29682/02_2025/8g2v_29682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g2v_29682/02_2025/8g2v_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_29682/02_2025/8g2v_29682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g2v_29682/02_2025/8g2v_29682.map" model { file = "/net/cci-nas-00/data/ceres_data/8g2v_29682/02_2025/8g2v_29682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g2v_29682/02_2025/8g2v_29682.cif" } resolution = 2.715 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 0.71, per 1000 atoms: 0.43 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: 1.65 Conformation dependent library (CDL) restraints added in 195.2 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: 0.29 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: 0.35 Time building geometry restraints manager: 1.69 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 3.030 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.120 Find NCS groups from input model: 0.040 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.530 ------------------------------------------------------------------------------- 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= 0.354 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TYR 0.005 0.001 TYR C 63 ARG 0.002 0.001 ARG I 74 *********************** 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 : 0.206 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: 1.3221 time to fit residues: 69.7960 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 : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.0670 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4880 r_free = 0.4880 target = 0.174735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.161441 restraints weight = 1709.778| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 1.92 r_work: 0.4612 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4493 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2057 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= 0.250 Angle : 0.568 4.372 2230 Z= 0.306 Chirality : 0.058 0.140 240 Planarity : 0.003 0.020 300 Dihedral : 5.068 11.689 220 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 8.33 % Allowed : 10.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.43), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR B 63 ARG 0.001 0.000 ARG B 74 *********************** 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 73 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.192 Fit side-chains REVERT: B 64 GLN cc_start: 0.8812 (mt0) cc_final: 0.8596 (mt0) REVERT: D 55 MET cc_start: 0.5258 (OUTLIER) cc_final: 0.3814 (tmt) REVERT: F 55 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.4353 (tmt) REVERT: H 55 MET cc_start: 0.5993 (OUTLIER) cc_final: 0.4631 (tmt) REVERT: I 74 ARG cc_start: 0.6715 (ttt-90) cc_final: 0.5761 (tpm170) REVERT: J 66 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7456 (mtmt) REVERT: J 74 ARG cc_start: 0.7028 (ttt-90) cc_final: 0.6147 (tpm170) outliers start: 15 outliers final: 2 residues processed: 64 average time/residue: 1.1758 time to fit residues: 76.4929 Evaluate side-chains 56 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 65 ASN ** C 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 67 ASN 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 = 0.4652 r_free = 0.4652 target = 0.156866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.141807 restraints weight = 1731.566| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 2.22 r_work: 0.4347 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4218 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1670 Z= 0.388 Angle : 0.628 4.868 2230 Z= 0.340 Chirality : 0.062 0.153 240 Planarity : 0.004 0.020 300 Dihedral : 5.278 12.996 220 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.00 % Allowed : 16.67 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.44), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR B 63 ARG 0.003 0.001 ARG I 74 *********************** 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: 9 poor density : 53 time to evaluate : 0.177 Fit side-chains REVERT: B 64 GLN cc_start: 0.8785 (mt0) cc_final: 0.8401 (mt0) REVERT: C 60 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8071 (mm-30) REVERT: D 60 GLU cc_start: 0.8057 (mp0) cc_final: 0.7478 (mp0) REVERT: F 64 GLN cc_start: 0.8743 (mt0) cc_final: 0.8448 (mt0) REVERT: G 60 GLU cc_start: 0.8041 (mp0) cc_final: 0.6473 (mp0) REVERT: H 55 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.4753 (tmt) REVERT: I 66 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7507 (mtmt) REVERT: J 60 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8358 (mm-30) outliers start: 9 outliers final: 2 residues processed: 58 average time/residue: 1.2593 time to fit residues: 74.3831 Evaluate side-chains 50 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.163488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.148461 restraints weight = 1652.520| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 2.16 r_work: 0.4432 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4304 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3009 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= 0.236 Angle : 0.559 4.334 2230 Z= 0.306 Chirality : 0.060 0.153 240 Planarity : 0.003 0.016 300 Dihedral : 4.956 11.795 220 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.56 % Allowed : 17.22 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.35), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYR I 63 ARG 0.001 0.000 ARG B 74 *********************** 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 64 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: B 64 GLN cc_start: 0.8784 (mt0) cc_final: 0.8369 (mt0) REVERT: C 60 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8098 (mm-30) REVERT: E 60 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8097 (mm-30) REVERT: F 64 GLN cc_start: 0.8710 (mt0) cc_final: 0.8427 (mt0) REVERT: H 64 GLN cc_start: 0.8717 (mt0) cc_final: 0.8487 (mt0) REVERT: J 60 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8245 (mm-30) REVERT: J 66 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7614 (mtmt) outliers start: 10 outliers final: 2 residues processed: 58 average time/residue: 1.3330 time to fit residues: 78.4942 Evaluate side-chains 51 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 60 GLU 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 7 optimal weight: 6.9990 chunk 18 optimal weight: 0.0370 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 = 0.4776 r_free = 0.4776 target = 0.168885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.154338 restraints weight = 1649.842| |-----------------------------------------------------------------------------| r_work (start): 0.4611 rms_B_bonded: 2.11 r_work: 0.4507 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4382 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1670 Z= 0.180 Angle : 0.547 4.561 2230 Z= 0.300 Chirality : 0.059 0.149 240 Planarity : 0.003 0.018 300 Dihedral : 4.777 11.993 220 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.44 % Allowed : 17.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.35), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYR E 63 ARG 0.000 0.000 ARG H 74 *********************** 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 56 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.215 Fit side-chains REVERT: B 64 GLN cc_start: 0.8746 (mt0) cc_final: 0.8362 (mt0) REVERT: C 60 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7735 (mm-30) REVERT: D 59 GLN cc_start: 0.8559 (mt0) cc_final: 0.8273 (mt0) REVERT: G 60 GLU cc_start: 0.7962 (mp0) cc_final: 0.6303 (mp0) REVERT: H 55 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.4656 (tmt) REVERT: J 60 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8146 (mm-30) REVERT: J 66 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7587 (mtmt) outliers start: 8 outliers final: 1 residues processed: 51 average time/residue: 1.3488 time to fit residues: 69.8387 Evaluate side-chains 49 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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** F 67 ASN G 64 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.169652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.154258 restraints weight = 1692.892| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 2.19 r_work: 0.4500 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4371 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1670 Z= 0.206 Angle : 0.550 3.917 2230 Z= 0.300 Chirality : 0.060 0.150 240 Planarity : 0.002 0.016 300 Dihedral : 4.748 11.854 220 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.44 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR I 63 ARG 0.001 0.000 ARG J 74 *********************** 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 56 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.210 Fit side-chains REVERT: B 64 GLN cc_start: 0.8704 (mt0) cc_final: 0.8327 (mt0) REVERT: C 60 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7693 (mm-30) REVERT: D 55 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4365 (tmt) REVERT: D 59 GLN cc_start: 0.8548 (mt0) cc_final: 0.8258 (mt0) REVERT: F 64 GLN cc_start: 0.8674 (mt0) cc_final: 0.8399 (mt0) REVERT: G 60 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: H 55 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.4639 (tmt) REVERT: J 60 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8135 (mm-30) outliers start: 8 outliers final: 2 residues processed: 51 average time/residue: 1.2543 time to fit residues: 64.9882 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 : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.167251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.152299 restraints weight = 1670.183| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 2.11 r_work: 0.4479 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4352 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1670 Z= 0.252 Angle : 0.569 4.196 2230 Z= 0.309 Chirality : 0.060 0.150 240 Planarity : 0.002 0.014 300 Dihedral : 4.864 13.644 220 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.44 % Allowed : 17.22 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.002 TYR E 63 ARG 0.001 0.000 ARG J 74 *********************** 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 52 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.191 Fit side-chains REVERT: C 60 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7713 (mm-30) REVERT: D 55 MET cc_start: 0.5196 (OUTLIER) cc_final: 0.4371 (tmt) REVERT: D 59 GLN cc_start: 0.8590 (mt0) cc_final: 0.8279 (mt0) REVERT: F 55 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.4540 (tmt) REVERT: F 64 GLN cc_start: 0.8669 (mt0) cc_final: 0.8323 (mt0) REVERT: G 60 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: H 55 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.4692 (tmt) REVERT: J 60 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8051 (mm-30) outliers start: 8 outliers final: 2 residues processed: 47 average time/residue: 1.1926 time to fit residues: 57.0633 Evaluate side-chains 48 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 G residue 60 GLU Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 0.0040 chunk 4 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.2168 ------------------------------------------------------------------------------- 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 ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 = 0.4887 r_free = 0.4887 target = 0.179122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.163606 restraints weight = 1613.390| |-----------------------------------------------------------------------------| r_work (start): 0.4740 rms_B_bonded: 2.11 r_work: 0.4627 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4499 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1670 Z= 0.169 Angle : 0.553 4.983 2230 Z= 0.303 Chirality : 0.060 0.153 240 Planarity : 0.002 0.014 300 Dihedral : 4.671 12.915 220 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.33 % Allowed : 19.44 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.50), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.001 TYR I 63 ARG 0.000 0.000 ARG F 74 *********************** 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 51 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.198 Fit side-chains REVERT: C 60 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7604 (mm-30) REVERT: D 55 MET cc_start: 0.5094 (OUTLIER) cc_final: 0.4397 (tmt) REVERT: D 59 GLN cc_start: 0.8411 (mt0) cc_final: 0.8157 (mt0) REVERT: F 55 MET cc_start: 0.5513 (OUTLIER) cc_final: 0.4551 (tmt) REVERT: G 60 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: H 55 MET cc_start: 0.6032 (OUTLIER) cc_final: 0.4589 (tmt) REVERT: I 60 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8097 (mp0) REVERT: I 74 ARG cc_start: 0.7244 (ttt-90) cc_final: 0.6170 (tpm170) REVERT: J 60 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8064 (mm-30) outliers start: 6 outliers final: 1 residues processed: 47 average time/residue: 1.2699 time to fit residues: 60.6659 Evaluate side-chains 47 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN G 64 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.173522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.158295 restraints weight = 1672.767| |-----------------------------------------------------------------------------| r_work (start): 0.4677 rms_B_bonded: 2.15 r_work: 0.4563 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4434 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1670 Z= 0.202 Angle : 0.557 4.585 2230 Z= 0.304 Chirality : 0.059 0.146 240 Planarity : 0.002 0.013 300 Dihedral : 4.759 12.772 220 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.78 % Allowed : 20.00 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.50), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR E 63 ARG 0.001 0.000 ARG I 74 *********************** 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 50 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.209 Fit side-chains REVERT: C 60 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7627 (mm-30) REVERT: D 55 MET cc_start: 0.5109 (OUTLIER) cc_final: 0.4341 (tmt) REVERT: D 59 GLN cc_start: 0.8470 (mt0) cc_final: 0.8193 (mt0) REVERT: F 55 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.4597 (tmt) REVERT: G 60 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: H 55 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.4620 (tmt) REVERT: I 60 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8168 (mp0) REVERT: J 60 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8065 (mm-30) outliers start: 5 outliers final: 1 residues processed: 46 average time/residue: 1.2620 time to fit residues: 59.0743 Evaluate side-chains 47 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 0.0570 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 B 67 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.170109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.154958 restraints weight = 1711.455| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 2.18 r_work: 0.4526 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4394 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1670 Z= 0.228 Angle : 0.571 4.826 2230 Z= 0.311 Chirality : 0.060 0.148 240 Planarity : 0.002 0.012 300 Dihedral : 4.839 13.126 220 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.33 % Allowed : 19.44 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.50), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR D 63 ARG 0.001 0.000 ARG J 74 ********************** 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 52 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: D 55 MET cc_start: 0.5071 (OUTLIER) cc_final: 0.4336 (tmt) REVERT: D 59 GLN cc_start: 0.8510 (mt0) cc_final: 0.8268 (mt0) REVERT: F 55 MET cc_start: 0.5564 (OUTLIER) cc_final: 0.4612 (tmt) REVERT: H 55 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.4598 (tmt) REVERT: I 60 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8044 (mp0) REVERT: J 60 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8132 (mm-30) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 1.2951 time to fit residues: 63.1824 Evaluate side-chains 47 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.171968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.156508 restraints weight = 1724.310| |-----------------------------------------------------------------------------| r_work (start): 0.4662 rms_B_bonded: 2.22 r_work: 0.4542 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4414 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1670 Z= 0.213 Angle : 0.592 5.061 2230 Z= 0.323 Chirality : 0.060 0.140 240 Planarity : 0.002 0.011 300 Dihedral : 4.844 12.272 220 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.78 % Allowed : 19.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.50), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR E 63 ARG 0.001 0.000 ARG I 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.62 seconds wall clock time: 42 minutes 17.71 seconds (2537.71 seconds total)