Starting phenix.real_space_refine on Wed Nov 13 22:57:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2024/8g2v_29682.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2024/8g2v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2024/8g2v_29682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2024/8g2v_29682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2024/8g2v_29682.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2024/8g2v_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-5513/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: 0.79, per 1000 atoms: 0.48 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: 1.40 Conformation dependent library (CDL) restraints added in 168.3 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: 0.48 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: 0.40 Time building geometry restraints manager: 1.43 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: 2.600 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.670 Find NCS groups from input model: 0.070 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.410 ------------------------------------------------------------------------------- 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 : 0.202 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: 1.3233 time to fit residues: 69.9539 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 : 0.204 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.203 Fit side-chains REVERT: B 64 GLN cc_start: 0.8756 (mt0) cc_final: 0.8532 (mt0) REVERT: D 55 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.4292 (tmt) REVERT: F 55 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.4565 (tmt) REVERT: H 55 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.4989 (tmt) REVERT: J 66 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7573 (mtmt) REVERT: J 74 ARG cc_start: 0.6881 (ttt-90) cc_final: 0.6588 (tpm170) outliers start: 15 outliers final: 2 residues processed: 64 average time/residue: 1.1550 time to fit residues: 75.1135 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 : 0.222 ------------------------------------------------------------------------------- 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 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.0070 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1670 Z= 0.193 Angle : 0.548 4.005 2230 Z= 0.298 Chirality : 0.059 0.141 240 Planarity : 0.003 0.016 300 Dihedral : 4.836 11.340 220 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.42 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: -3.54 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.35), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 63 ARG 0.001 0.000 ARG B 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 63 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.208 Fit side-chains REVERT: B 60 GLU cc_start: 0.8027 (mp0) cc_final: 0.6536 (mp0) REVERT: C 60 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7567 (mm-30) REVERT: D 60 GLU cc_start: 0.7905 (mp0) cc_final: 0.7021 (mp0) REVERT: G 60 GLU cc_start: 0.7792 (mp0) cc_final: 0.6509 (mp0) REVERT: I 66 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7626 (mtmt) REVERT: J 66 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7618 (mtmt) REVERT: J 74 ARG cc_start: 0.7002 (ttt-90) cc_final: 0.6679 (tpm170) outliers start: 10 outliers final: 3 residues processed: 57 average time/residue: 1.2657 time to fit residues: 73.2599 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 : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain E 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2929 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= 0.209 Angle : 0.544 3.996 2230 Z= 0.296 Chirality : 0.059 0.145 240 Planarity : 0.003 0.028 300 Dihedral : 4.790 11.474 220 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.00 % Allowed : 18.89 % Favored : 76.11 % 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: -3.52 (0.48), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR B 63 ARG 0.001 0.000 ARG J 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 61 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.167 Fit side-chains REVERT: B 60 GLU cc_start: 0.7922 (mp0) cc_final: 0.6202 (mp0) REVERT: B 64 GLN cc_start: 0.8694 (mt0) cc_final: 0.8363 (mt0) REVERT: C 60 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 60 GLU cc_start: 0.7712 (mp0) cc_final: 0.7215 (mp0) REVERT: G 60 GLU cc_start: 0.7783 (mp0) cc_final: 0.6315 (mp0) REVERT: H 55 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.4985 (tmt) REVERT: I 66 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7653 (mtmt) REVERT: J 74 ARG cc_start: 0.7086 (ttt-90) cc_final: 0.6733 (tpm170) outliers start: 9 outliers final: 1 residues processed: 56 average time/residue: 1.4506 time to fit residues: 82.3690 Evaluate side-chains 52 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 64 GLN F 67 ASN G 64 GLN H 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3109 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= 0.225 Angle : 0.548 4.393 2230 Z= 0.298 Chirality : 0.059 0.146 240 Planarity : 0.003 0.019 300 Dihedral : 4.781 11.927 220 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.00 % Allowed : 18.33 % 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 (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: -3.41 (0.48), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR A 63 ARG 0.001 0.000 ARG J 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 58 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.199 Fit side-chains REVERT: C 60 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7759 (mm-30) REVERT: D 55 MET cc_start: 0.5723 (OUTLIER) cc_final: 0.4749 (tmt) REVERT: G 60 GLU cc_start: 0.7724 (mp0) cc_final: 0.6139 (mp0) REVERT: H 55 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.4970 (tmt) REVERT: I 66 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7663 (mtmt) outliers start: 9 outliers final: 1 residues processed: 53 average time/residue: 1.4815 time to fit residues: 79.6320 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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 2 optimal weight: 0.0060 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3388 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= 0.198 Angle : 0.527 4.137 2230 Z= 0.288 Chirality : 0.059 0.147 240 Planarity : 0.002 0.016 300 Dihedral : 4.707 12.895 220 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.67 % Allowed : 18.33 % Favored : 75.00 % 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: -3.44 (0.48), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 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 59 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.210 Fit side-chains REVERT: C 60 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7723 (mm-30) REVERT: H 55 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.4956 (tmt) REVERT: I 66 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7673 (mtmt) REVERT: J 60 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: J 66 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7634 (mtmt) outliers start: 12 outliers final: 1 residues processed: 50 average time/residue: 1.4174 time to fit residues: 71.8624 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain J residue 60 GLU 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 3 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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** F 67 ASN G 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1670 Z= 0.256 Angle : 0.551 4.238 2230 Z= 0.301 Chirality : 0.060 0.151 240 Planarity : 0.002 0.013 300 Dihedral : 4.879 12.779 220 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.56 % Allowed : 20.00 % 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 (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: -3.38 (0.48), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 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 59 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.187 Fit side-chains REVERT: D 55 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.4841 (tmt) REVERT: F 55 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.4949 (tmt) REVERT: G 60 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6967 (mp0) REVERT: H 55 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.4875 (tmt) REVERT: J 66 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7652 (mtmt) outliers start: 10 outliers final: 1 residues processed: 53 average time/residue: 1.4157 time to fit residues: 76.0766 Evaluate side-chains 52 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 66 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.0370 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1670 Z= 0.213 Angle : 0.631 6.113 2230 Z= 0.341 Chirality : 0.059 0.139 240 Planarity : 0.002 0.013 300 Dihedral : 4.897 13.006 220 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.33 % Allowed : 24.44 % Favored : 72.22 % 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: -3.34 (0.48), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYR I 63 ARG 0.001 0.000 ARG J 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 54 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.201 Fit side-chains REVERT: D 55 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.4829 (tmt) REVERT: F 55 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.4922 (tmt) REVERT: H 55 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.4870 (tmt) outliers start: 6 outliers final: 1 residues processed: 50 average time/residue: 1.2983 time to fit residues: 65.9154 Evaluate side-chains 52 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 2 optimal weight: 0.0980 chunk 15 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 0.2616 ------------------------------------------------------------------------------- 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** F 67 ASN G 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1670 Z= 0.197 Angle : 0.631 5.619 2230 Z= 0.343 Chirality : 0.060 0.146 240 Planarity : 0.002 0.010 300 Dihedral : 4.859 13.191 220 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.22 % Allowed : 26.11 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.28 (0.49), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR G 63 ARG 0.000 0.000 ARG F 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 54 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.201 Fit side-chains REVERT: D 55 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.4817 (tmt) REVERT: F 55 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.4916 (tmt) REVERT: H 55 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.4830 (tmt) outliers start: 4 outliers final: 0 residues processed: 51 average time/residue: 1.2791 time to fit residues: 66.2445 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 : 0.180 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** B 67 ASN D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN G 64 GLN H 67 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1670 Z= 0.244 Angle : 0.631 5.987 2230 Z= 0.343 Chirality : 0.060 0.144 240 Planarity : 0.002 0.013 300 Dihedral : 5.034 13.705 220 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.33 % Allowed : 25.00 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.25 (0.49), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.37), 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 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: 6 poor density : 44 time to evaluate : 0.184 Fit side-chains REVERT: D 55 MET cc_start: 0.5586 (OUTLIER) cc_final: 0.4751 (tmt) REVERT: F 55 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.4987 (tmt) REVERT: G 60 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7588 (mm-30) REVERT: H 55 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.4840 (tmt) outliers start: 6 outliers final: 1 residues processed: 47 average time/residue: 1.1797 time to fit residues: 56.4070 Evaluate side-chains 46 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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** G 64 GLN ** 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 = 0.4834 r_free = 0.4834 target = 0.171016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.156644 restraints weight = 1687.275| |-----------------------------------------------------------------------------| r_work (start): 0.4674 rms_B_bonded: 2.09 r_work: 0.4567 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4444 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1670 Z= 0.238 Angle : 0.652 6.191 2230 Z= 0.354 Chirality : 0.060 0.146 240 Planarity : 0.002 0.012 300 Dihedral : 5.059 13.453 220 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.89 % Allowed : 24.44 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.19 (0.50), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 63 ARG 0.001 0.000 ARG J 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.51 seconds wall clock time: 38 minutes 56.60 seconds (2336.60 seconds total)