Starting phenix.real_space_refine on Fri Mar 15 09:43:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/03_2024/5o3t_3743.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/03_2024/5o3t_3743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/03_2024/5o3t_3743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/03_2024/5o3t_3743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/03_2024/5o3t_3743.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/03_2024/5o3t_3743.pdb" } resolution = 3.4 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: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 H 5790 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11360 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 5.16, per 1000 atoms: 0.45 Number of scatterers: 11360 At special positions: 0 Unit cell: (116.48, 114.4, 46.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 1040 8.00 N 1010 7.00 C 3510 6.00 H 5790 1.00 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 - 3.50 Amino acid : False - 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: 8.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5780 1.03 - 1.22: 10 1.22 - 1.41: 2130 1.41 - 1.60: 3520 1.60 - 1.79: 10 Bond restraints: 11450 Sorted by residual: bond pdb=" C VAL G 363 " pdb=" N PRO G 364 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.11e-02 8.12e+03 1.89e+00 bond pdb=" C VAL F 363 " pdb=" N PRO F 364 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.11e-02 8.12e+03 1.76e+00 bond pdb=" C VAL H 363 " pdb=" N PRO H 364 " ideal model delta sigma weight residual 1.334 1.319 0.014 1.11e-02 8.12e+03 1.70e+00 bond pdb=" C VAL C 363 " pdb=" N PRO C 364 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.11e-02 8.12e+03 1.63e+00 bond pdb=" C VAL J 363 " pdb=" N PRO J 364 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.11e-02 8.12e+03 1.54e+00 ... (remaining 11445 not shown) Histogram of bond angle deviations from ideal: 102.83 - 108.58: 3334 108.58 - 114.34: 11963 114.34 - 120.09: 2033 120.09 - 125.84: 3401 125.84 - 131.59: 169 Bond angle restraints: 20900 Sorted by residual: angle pdb=" N LYS I 331 " pdb=" CA LYS I 331 " pdb=" C LYS I 331 " ideal model delta sigma weight residual 108.97 116.78 -7.81 1.82e+00 3.02e-01 1.84e+01 angle pdb=" N LYS E 331 " pdb=" CA LYS E 331 " pdb=" C LYS E 331 " ideal model delta sigma weight residual 108.97 116.78 -7.81 1.82e+00 3.02e-01 1.84e+01 angle pdb=" N LYS C 331 " pdb=" CA LYS C 331 " pdb=" C LYS C 331 " ideal model delta sigma weight residual 108.97 116.75 -7.78 1.82e+00 3.02e-01 1.83e+01 angle pdb=" N LYS A 331 " pdb=" CA LYS A 331 " pdb=" C LYS A 331 " ideal model delta sigma weight residual 108.97 116.75 -7.78 1.82e+00 3.02e-01 1.83e+01 angle pdb=" N LYS G 331 " pdb=" CA LYS G 331 " pdb=" C LYS G 331 " ideal model delta sigma weight residual 108.97 116.74 -7.77 1.82e+00 3.02e-01 1.82e+01 ... (remaining 20895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.52: 4578 10.52 - 21.04: 327 21.04 - 31.56: 195 31.56 - 42.09: 80 42.09 - 52.61: 90 Dihedral angle restraints: 5270 sinusoidal: 3000 harmonic: 2270 Sorted by residual: dihedral pdb=" CA LEU E 315 " pdb=" C LEU E 315 " pdb=" N SER E 316 " pdb=" CA SER E 316 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU F 315 " pdb=" C LEU F 315 " pdb=" N SER F 316 " pdb=" CA SER F 316 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU C 315 " pdb=" C LEU C 315 " pdb=" N SER C 316 " pdb=" CA SER C 316 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 390 0.027 - 0.054: 216 0.054 - 0.081: 114 0.081 - 0.108: 78 0.108 - 0.135: 62 Chirality restraints: 860 Sorted by residual: chirality pdb=" CA LYS C 331 " pdb=" N LYS C 331 " pdb=" C LYS C 331 " pdb=" CB LYS C 331 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE E 328 " pdb=" N ILE E 328 " pdb=" C ILE E 328 " pdb=" CB ILE E 328 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE F 328 " pdb=" N ILE F 328 " pdb=" C ILE F 328 " pdb=" CB ILE F 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 857 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 363 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO B 364 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 363 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO D 364 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 364 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 363 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO G 364 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 364 " -0.024 5.00e-02 4.00e+02 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.91: 171 1.91 - 2.58: 12948 2.58 - 3.26: 33858 3.26 - 3.93: 42845 3.93 - 4.60: 66195 Nonbonded interactions: 156017 Sorted by model distance: nonbonded pdb=" HB3 HIS F 329 " pdb=" HE3 LYS F 331 " model vdw 1.242 2.440 nonbonded pdb=" HB3 HIS B 329 " pdb=" HE3 LYS B 331 " model vdw 1.242 2.440 nonbonded pdb=" HB3 HIS J 329 " pdb=" HE3 LYS J 331 " model vdw 1.242 2.440 nonbonded pdb=" HB3 HIS D 329 " pdb=" HE3 LYS D 331 " model vdw 1.243 2.440 nonbonded pdb=" HB3 HIS H 329 " pdb=" HE3 LYS H 331 " model vdw 1.243 2.440 ... (remaining 156012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.050 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: 0.160 Extract box with map and model: 4.540 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.720 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 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 : 0.007 0.053 5660 Z= 0.273 Angle : 0.915 7.811 7580 Z= 0.472 Chirality : 0.055 0.135 860 Planarity : 0.005 0.043 960 Dihedral : 10.151 50.514 2160 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Rotamer: Outliers : 1.56 % Allowed : 3.12 % Favored : 95.31 % 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: -6.47 (0.15), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 374 PHE 0.007 0.001 PHE D 346 TYR 0.005 0.003 TYR C 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.6710 (mp) cc_final: 0.6451 (mt) REVERT: D 360 ILE cc_start: 0.5942 (mp) cc_final: 0.5679 (mt) REVERT: G 331 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7618 (mttt) outliers start: 10 outliers final: 5 residues processed: 154 average time/residue: 0.6276 time to fit residues: 113.6980 Evaluate side-chains 88 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS E 362 HIS G 351 GLN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5660 Z= 0.160 Angle : 0.647 4.344 7580 Z= 0.328 Chirality : 0.051 0.135 860 Planarity : 0.004 0.033 960 Dihedral : 7.779 49.625 764 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 1.88 % Allowed : 9.53 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.93 (0.17), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 329 PHE 0.022 0.001 PHE J 346 TYR 0.009 0.003 TYR I 310 ARG 0.003 0.000 ARG J 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5626 (OUTLIER) cc_final: 0.5140 (mmmt) REVERT: B 360 ILE cc_start: 0.6862 (mp) cc_final: 0.6619 (mt) REVERT: F 360 ILE cc_start: 0.6783 (mp) cc_final: 0.6521 (mt) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.4385 time to fit residues: 51.7831 Evaluate side-chains 82 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 HIS ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5660 Z= 0.125 Angle : 0.567 4.210 7580 Z= 0.288 Chirality : 0.049 0.126 860 Planarity : 0.003 0.024 960 Dihedral : 6.891 46.969 756 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 1.41 % Allowed : 10.62 % Favored : 87.97 % 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: -5.58 (0.19), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 330 PHE 0.026 0.002 PHE F 346 TYR 0.006 0.002 TYR I 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.6989 (mp) cc_final: 0.6733 (mt) REVERT: F 360 ILE cc_start: 0.6912 (mp) cc_final: 0.6693 (mt) REVERT: G 346 PHE cc_start: 0.6618 (m-10) cc_final: 0.6331 (m-10) REVERT: H 338 GLU cc_start: 0.3918 (mp0) cc_final: 0.3186 (pm20) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.4005 time to fit residues: 46.7818 Evaluate side-chains 75 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain H residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.0000 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5660 Z= 0.121 Angle : 0.534 3.863 7580 Z= 0.272 Chirality : 0.049 0.129 860 Planarity : 0.003 0.025 960 Dihedral : 6.310 48.646 748 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 2.03 % Allowed : 10.31 % Favored : 87.66 % 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: -5.31 (0.21), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 330 PHE 0.021 0.001 PHE F 346 TYR 0.007 0.002 TYR C 310 ARG 0.002 0.001 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5232 (OUTLIER) cc_final: 0.3920 (mmtm) REVERT: B 360 ILE cc_start: 0.7192 (mp) cc_final: 0.6894 (mt) REVERT: F 360 ILE cc_start: 0.6928 (mp) cc_final: 0.6679 (mt) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.4417 time to fit residues: 47.3040 Evaluate side-chains 79 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS J 362 HIS J 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5660 Z= 0.191 Angle : 0.605 5.267 7580 Z= 0.310 Chirality : 0.050 0.130 860 Planarity : 0.003 0.029 960 Dihedral : 6.887 52.299 748 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 3.28 % Allowed : 10.31 % Favored : 86.41 % 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: -5.33 (0.21), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 374 PHE 0.015 0.002 PHE E 346 TYR 0.009 0.003 TYR I 310 ARG 0.004 0.001 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5629 (OUTLIER) cc_final: 0.4221 (mmtm) REVERT: B 360 ILE cc_start: 0.7104 (mp) cc_final: 0.6851 (mt) REVERT: H 338 GLU cc_start: 0.3896 (mp0) cc_final: 0.3193 (pm20) REVERT: I 363 VAL cc_start: 0.8604 (t) cc_final: 0.8326 (t) outliers start: 21 outliers final: 16 residues processed: 99 average time/residue: 0.3871 time to fit residues: 49.6141 Evaluate side-chains 93 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 HIS H 362 HIS ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.6672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5660 Z= 0.189 Angle : 0.589 3.952 7580 Z= 0.303 Chirality : 0.050 0.136 860 Planarity : 0.003 0.031 960 Dihedral : 6.964 55.018 748 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.94 % Favored : 86.06 % Rotamer: Outliers : 2.81 % Allowed : 13.44 % Favored : 83.75 % 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: -5.30 (0.21), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 374 PHE 0.017 0.001 PHE A 346 TYR 0.009 0.002 TYR I 310 ARG 0.003 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5581 (OUTLIER) cc_final: 0.4797 (mmmt) REVERT: B 360 ILE cc_start: 0.7258 (mp) cc_final: 0.7029 (mt) REVERT: D 354 ILE cc_start: 0.5147 (mm) cc_final: 0.4896 (mt) REVERT: I 363 VAL cc_start: 0.8647 (t) cc_final: 0.8370 (t) outliers start: 18 outliers final: 17 residues processed: 91 average time/residue: 0.4153 time to fit residues: 48.6466 Evaluate side-chains 92 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5660 Z= 0.159 Angle : 0.555 4.075 7580 Z= 0.285 Chirality : 0.049 0.158 860 Planarity : 0.003 0.028 960 Dihedral : 6.745 58.020 748 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.23 % Favored : 85.77 % Rotamer: Outliers : 2.50 % Allowed : 13.28 % Favored : 84.22 % 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: -5.24 (0.21), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 374 PHE 0.014 0.001 PHE A 346 TYR 0.010 0.002 TYR I 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.4450 (mmtm) REVERT: B 360 ILE cc_start: 0.7310 (mp) cc_final: 0.7057 (mt) REVERT: F 354 ILE cc_start: 0.4804 (mm) cc_final: 0.4598 (mt) REVERT: I 363 VAL cc_start: 0.8617 (t) cc_final: 0.8352 (t) REVERT: J 354 ILE cc_start: 0.6465 (tp) cc_final: 0.6243 (mm) outliers start: 16 outliers final: 15 residues processed: 90 average time/residue: 0.3710 time to fit residues: 43.6720 Evaluate side-chains 92 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.7168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5660 Z= 0.138 Angle : 0.541 4.720 7580 Z= 0.276 Chirality : 0.049 0.148 860 Planarity : 0.003 0.027 960 Dihedral : 6.623 58.946 748 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 2.66 % Allowed : 14.22 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.12 (0.21), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 330 PHE 0.014 0.001 PHE A 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5802 (OUTLIER) cc_final: 0.4457 (mmtm) REVERT: D 354 ILE cc_start: 0.5153 (mm) cc_final: 0.4854 (mt) REVERT: H 338 GLU cc_start: 0.3936 (mp0) cc_final: 0.3351 (pm20) outliers start: 17 outliers final: 14 residues processed: 91 average time/residue: 0.3715 time to fit residues: 44.0788 Evaluate side-chains 89 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain H residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5660 Z= 0.125 Angle : 0.524 4.003 7580 Z= 0.267 Chirality : 0.049 0.138 860 Planarity : 0.003 0.026 960 Dihedral : 6.414 58.944 748 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % Rotamer: Outliers : 2.34 % Allowed : 14.69 % Favored : 82.97 % 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: -5.03 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 374 PHE 0.011 0.001 PHE A 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.4459 (mmtm) REVERT: D 354 ILE cc_start: 0.5046 (mm) cc_final: 0.4819 (mt) REVERT: H 338 GLU cc_start: 0.3945 (mp0) cc_final: 0.3374 (pm20) outliers start: 15 outliers final: 14 residues processed: 83 average time/residue: 0.4041 time to fit residues: 43.9017 Evaluate side-chains 87 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5660 Z= 0.113 Angle : 0.517 4.034 7580 Z= 0.262 Chirality : 0.048 0.130 860 Planarity : 0.003 0.025 960 Dihedral : 6.245 56.937 748 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 2.34 % Allowed : 15.16 % Favored : 82.50 % 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: -4.96 (0.21), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 330 PHE 0.013 0.001 PHE D 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG I 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5726 (OUTLIER) cc_final: 0.4473 (mmtm) REVERT: D 338 GLU cc_start: 0.3348 (mp0) cc_final: 0.3011 (mp0) REVERT: H 338 GLU cc_start: 0.3903 (mp0) cc_final: 0.3273 (pm20) REVERT: H 354 ILE cc_start: 0.4670 (mp) cc_final: 0.4236 (mt) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.3751 time to fit residues: 42.2991 Evaluate side-chains 86 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.185074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.136419 restraints weight = 20287.855| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 2.97 r_work: 0.4438 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.4339 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5660 Z= 0.115 Angle : 0.511 3.829 7580 Z= 0.260 Chirality : 0.048 0.132 860 Planarity : 0.003 0.024 960 Dihedral : 5.858 54.610 744 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 2.03 % Allowed : 15.31 % Favored : 82.66 % 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: -4.91 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.011 0.001 PHE J 346 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3670.14 seconds wall clock time: 65 minutes 26.10 seconds (3926.10 seconds total)