Starting phenix.real_space_refine on Tue Jul 29 06:58:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5o3t_3743/07_2025/5o3t_3743.cif Found real_map, /net/cci-nas-00/data/ceres_data/5o3t_3743/07_2025/5o3t_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/cci-nas-00/data/ceres_data/5o3t_3743/07_2025/5o3t_3743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5o3t_3743/07_2025/5o3t_3743.map" model { file = "/net/cci-nas-00/data/ceres_data/5o3t_3743/07_2025/5o3t_3743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5o3t_3743/07_2025/5o3t_3743.cif" } 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. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.71, per 1000 atoms: 0.50 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 - 3.00 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: 2.92 Conformation dependent library (CDL) restraints added in 733.2 milliseconds 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: 1.43 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: 3.53 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: 0.00 - 1.56: 17684 1.56 - 3.12: 2803 3.12 - 4.69: 383 4.69 - 6.25: 10 6.25 - 7.81: 20 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 Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.190 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 22.900 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- 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 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 5660) covalent geometry : angle 0.91542 ( 7580) *********************** 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 to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.946 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: 0.6104 time to fit residues: 110.1237 Evaluate side-chains 88 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 362 HIS G 351 GLN ** I 330 HIS ** 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 = 0.5064 r_free = 0.5064 target = 0.206077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.153644 restraints weight = 19337.000| |-----------------------------------------------------------------------------| r_work (start): 0.4686 rms_B_bonded: 3.21 r_work: 0.4592 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5660 Z= 0.155 Angle : 0.650 4.617 7580 Z= 0.332 Chirality : 0.051 0.134 860 Planarity : 0.004 0.028 960 Dihedral : 7.764 49.325 764 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 1.72 % Allowed : 9.84 % Favored : 88.44 % 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: -6.01 (0.17), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 374 PHE 0.020 0.001 PHE J 346 TYR 0.009 0.003 TYR I 310 ARG 0.002 0.000 ARG J 349 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5660) covalent geometry : angle 0.65030 ( 7580) *********************** 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.848 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: A 338 GLU cc_start: 0.6385 (tp30) cc_final: 0.5494 (tm-30) REVERT: A 347 LYS cc_start: 0.7874 (mttt) cc_final: 0.7637 (mttp) REVERT: A 369 LYS cc_start: 0.7785 (tttt) cc_final: 0.7379 (tttm) REVERT: B 331 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.4683 (mmmt) REVERT: C 338 GLU cc_start: 0.6945 (tp30) cc_final: 0.5325 (tp30) REVERT: C 347 LYS cc_start: 0.8072 (mttt) cc_final: 0.7824 (mttp) REVERT: E 338 GLU cc_start: 0.6659 (tp30) cc_final: 0.6265 (tp30) REVERT: E 357 LEU cc_start: 0.8774 (tp) cc_final: 0.8469 (tt) REVERT: F 338 GLU cc_start: 0.4145 (mp0) cc_final: 0.3612 (mp0) REVERT: F 346 PHE cc_start: 0.7099 (m-10) cc_final: 0.6882 (m-80) REVERT: G 338 GLU cc_start: 0.7011 (tp30) cc_final: 0.6793 (tp30) REVERT: G 353 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7752 (ttpp) REVERT: G 357 LEU cc_start: 0.8830 (tt) cc_final: 0.8570 (tt) REVERT: G 369 LYS cc_start: 0.7600 (mtpt) cc_final: 0.7253 (mtpp) REVERT: J 339 VAL cc_start: 0.5287 (t) cc_final: 0.4832 (p) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.4718 time to fit residues: 60.4415 Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE 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 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 12 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS F 359 ASN F 362 HIS H 362 HIS ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS J 359 ASN J 362 HIS J 368 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.199643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.148735 restraints weight = 19806.980| |-----------------------------------------------------------------------------| r_work (start): 0.4624 rms_B_bonded: 3.06 r_work: 0.4514 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5660 Z= 0.185 Angle : 0.617 4.321 7580 Z= 0.317 Chirality : 0.050 0.130 860 Planarity : 0.003 0.024 960 Dihedral : 7.474 49.512 756 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 1.88 % Allowed : 11.88 % Favored : 86.25 % 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: -5.77 (0.19), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.39 (0.14), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 330 PHE 0.017 0.002 PHE E 346 TYR 0.009 0.003 TYR I 310 ARG 0.003 0.000 ARG H 349 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 5660) covalent geometry : angle 0.61655 ( 7580) *********************** 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.6413 (tp30) cc_final: 0.6158 (tm-30) REVERT: A 347 LYS cc_start: 0.8023 (mttt) cc_final: 0.7765 (mttp) REVERT: A 369 LYS cc_start: 0.7892 (tttt) cc_final: 0.7484 (tttm) REVERT: B 331 LYS cc_start: 0.6067 (OUTLIER) cc_final: 0.3836 (mmtm) REVERT: C 338 GLU cc_start: 0.7183 (tp30) cc_final: 0.6796 (mp0) REVERT: C 345 ASP cc_start: 0.7337 (t0) cc_final: 0.6990 (t0) REVERT: C 347 LYS cc_start: 0.8272 (mttt) cc_final: 0.7968 (mttp) REVERT: C 356 SER cc_start: 0.8189 (t) cc_final: 0.7768 (m) REVERT: F 360 ILE cc_start: 0.8192 (mt) cc_final: 0.7857 (mp) REVERT: G 353 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7870 (ttpp) REVERT: G 357 LEU cc_start: 0.8818 (tt) cc_final: 0.8490 (tt) REVERT: G 369 LYS cc_start: 0.7574 (mtpt) cc_final: 0.7310 (ttpp) REVERT: I 346 PHE cc_start: 0.7763 (m-10) cc_final: 0.7090 (m-10) REVERT: J 368 ASN cc_start: 0.7561 (m110) cc_final: 0.7223 (m-40) outliers start: 12 outliers final: 7 residues processed: 102 average time/residue: 0.4445 time to fit residues: 57.0766 Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE 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 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 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.194433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.143361 restraints weight = 19957.648| |-----------------------------------------------------------------------------| r_work (start): 0.4594 rms_B_bonded: 3.13 r_work: 0.4502 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5660 Z= 0.152 Angle : 0.565 4.269 7580 Z= 0.291 Chirality : 0.049 0.154 860 Planarity : 0.003 0.027 960 Dihedral : 7.008 51.104 752 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 1.56 % Allowed : 12.97 % Favored : 85.47 % 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: -5.53 (0.19), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.012 0.001 PHE E 346 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5660) covalent geometry : angle 0.56505 ( 7580) *********************** 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 95 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.5996 (tp30) cc_final: 0.5459 (tm-30) REVERT: A 369 LYS cc_start: 0.7916 (tttt) cc_final: 0.7521 (tttm) REVERT: B 331 LYS cc_start: 0.6148 (OUTLIER) cc_final: 0.3975 (mmtm) REVERT: G 353 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7748 (ttpp) REVERT: G 357 LEU cc_start: 0.8839 (tt) cc_final: 0.8529 (tt) REVERT: G 369 LYS cc_start: 0.7572 (mtpt) cc_final: 0.7279 (ttpp) REVERT: H 338 GLU cc_start: 0.4823 (pm20) cc_final: 0.4442 (pm20) REVERT: I 346 PHE cc_start: 0.7728 (m-10) cc_final: 0.7105 (m-10) REVERT: J 368 ASN cc_start: 0.7512 (m110) cc_final: 0.7285 (m-40) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.5379 time to fit residues: 63.5114 Evaluate side-chains 79 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 0.0270 chunk 53 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.192486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.142133 restraints weight = 18999.487| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 2.97 r_work: 0.4489 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.4382 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5660 Z= 0.104 Angle : 0.520 3.949 7580 Z= 0.265 Chirality : 0.049 0.136 860 Planarity : 0.003 0.027 960 Dihedral : 6.627 52.562 752 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.88 % Allowed : 13.28 % Favored : 84.84 % 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: -5.26 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.017 0.001 PHE D 346 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5660) covalent geometry : angle 0.51976 ( 7580) *********************** 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 97 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.7823 (tttt) cc_final: 0.7349 (tttp) REVERT: B 331 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.3893 (mmtm) REVERT: C 338 GLU cc_start: 0.7081 (tp30) cc_final: 0.6366 (mp0) REVERT: D 354 ILE cc_start: 0.7226 (mt) cc_final: 0.6937 (mm) REVERT: E 342 GLU cc_start: 0.6987 (mp0) cc_final: 0.6777 (mp0) REVERT: F 360 ILE cc_start: 0.8006 (mt) cc_final: 0.7620 (mp) REVERT: G 353 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7607 (ttpp) REVERT: G 357 LEU cc_start: 0.8750 (tt) cc_final: 0.8408 (tt) REVERT: G 369 LYS cc_start: 0.7502 (mtpt) cc_final: 0.7211 (ttpp) REVERT: I 346 PHE cc_start: 0.7693 (m-10) cc_final: 0.7021 (m-10) REVERT: J 368 ASN cc_start: 0.7472 (m110) cc_final: 0.6862 (m-40) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.4311 time to fit residues: 52.2881 Evaluate side-chains 81 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 371 ILE Chi-restraints excluded: chain H residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.0020 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.181283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.130816 restraints weight = 19997.006| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 3.11 r_work: 0.4394 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.4280 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.6487 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= 0.178 Angle : 0.577 6.061 7580 Z= 0.295 Chirality : 0.050 0.138 860 Planarity : 0.003 0.027 960 Dihedral : 7.038 55.590 752 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 1.72 % Allowed : 15.31 % 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: -5.29 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 374 PHE 0.014 0.001 PHE D 346 TYR 0.009 0.003 TYR E 310 ARG 0.002 0.000 ARG D 349 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5660) covalent geometry : angle 0.57670 ( 7580) *********************** 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 90 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6214 (OUTLIER) cc_final: 0.4034 (mmtm) REVERT: D 354 ILE cc_start: 0.7173 (mt) cc_final: 0.6901 (mm) REVERT: E 342 GLU cc_start: 0.7033 (mp0) cc_final: 0.6787 (mp0) REVERT: G 346 PHE cc_start: 0.7485 (m-10) cc_final: 0.7276 (m-10) REVERT: G 353 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7532 (ttpp) REVERT: G 357 LEU cc_start: 0.8729 (tt) cc_final: 0.8315 (tt) REVERT: G 369 LYS cc_start: 0.7613 (mtpt) cc_final: 0.7254 (ttpp) REVERT: H 338 GLU cc_start: 0.4822 (pm20) cc_final: 0.4569 (pm20) REVERT: I 346 PHE cc_start: 0.7645 (m-10) cc_final: 0.6965 (m-10) REVERT: J 354 ILE cc_start: 0.7364 (mm) cc_final: 0.7003 (tp) outliers start: 11 outliers final: 10 residues processed: 89 average time/residue: 0.4100 time to fit residues: 47.2226 Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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 371 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 HIS ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.183059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.132396 restraints weight = 19540.196| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 2.98 r_work: 0.4350 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4240 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.6940 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= 0.197 Angle : 0.585 4.547 7580 Z= 0.303 Chirality : 0.050 0.135 860 Planarity : 0.003 0.028 960 Dihedral : 7.338 59.886 752 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.80 % Favored : 86.20 % Rotamer: Outliers : 2.34 % Allowed : 15.00 % 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: -5.28 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 374 PHE 0.020 0.002 PHE A 346 TYR 0.009 0.003 TYR E 310 ARG 0.002 0.000 ARG D 349 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 5660) covalent geometry : angle 0.58532 ( 7580) *********************** 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 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6287 (OUTLIER) cc_final: 0.4736 (mmmt) REVERT: E 342 GLU cc_start: 0.7125 (mp0) cc_final: 0.6674 (mp0) REVERT: G 338 GLU cc_start: 0.7237 (tp30) cc_final: 0.6921 (tm-30) REVERT: G 346 PHE cc_start: 0.7551 (m-10) cc_final: 0.7248 (m-10) REVERT: G 353 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7483 (ttpp) REVERT: G 357 LEU cc_start: 0.8780 (tt) cc_final: 0.8418 (tt) REVERT: G 369 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7334 (ttpp) REVERT: I 346 PHE cc_start: 0.7732 (m-10) cc_final: 0.7283 (m-10) outliers start: 15 outliers final: 13 residues processed: 101 average time/residue: 0.4398 time to fit residues: 56.9187 Evaluate side-chains 90 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 D residue 356 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4976 r_free = 0.4976 target = 0.177921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.128820 restraints weight = 20014.077| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 3.09 r_work: 0.4373 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.4264 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.7187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5660 Z= 0.153 Angle : 0.564 4.110 7580 Z= 0.290 Chirality : 0.050 0.165 860 Planarity : 0.003 0.027 960 Dihedral : 6.826 56.769 748 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 2.50 % Allowed : 17.03 % Favored : 80.47 % 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: -5.17 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.013 0.001 PHE A 346 TYR 0.009 0.002 TYR A 310 ARG 0.002 0.000 ARG D 349 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5660) covalent geometry : angle 0.56377 ( 7580) *********************** 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 94 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.4335 (mmtt) REVERT: E 342 GLU cc_start: 0.7040 (mp0) cc_final: 0.6779 (mp0) REVERT: G 338 GLU cc_start: 0.7237 (tp30) cc_final: 0.6881 (tm-30) REVERT: G 353 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7349 (ttpp) REVERT: G 357 LEU cc_start: 0.8767 (tt) cc_final: 0.8401 (tt) REVERT: H 338 GLU cc_start: 0.4883 (pm20) cc_final: 0.4406 (pm20) REVERT: I 346 PHE cc_start: 0.7670 (m-10) cc_final: 0.7226 (m-10) outliers start: 16 outliers final: 14 residues processed: 93 average time/residue: 0.4632 time to fit residues: 56.4340 Evaluate side-chains 87 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 331 LYS Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.173587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.125215 restraints weight = 20487.248| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 3.05 r_work: 0.4335 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.4228 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.7532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5660 Z= 0.219 Angle : 0.612 4.621 7580 Z= 0.318 Chirality : 0.051 0.145 860 Planarity : 0.003 0.028 960 Dihedral : 7.073 58.698 748 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.90 % Favored : 83.10 % Rotamer: Outliers : 2.66 % Allowed : 17.81 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.19 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 374 PHE 0.017 0.001 PHE A 346 TYR 0.010 0.003 TYR I 310 ARG 0.002 0.000 ARG F 349 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 5660) covalent geometry : angle 0.61231 ( 7580) *********************** 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.4519 (mmtt) REVERT: E 342 GLU cc_start: 0.7196 (mp0) cc_final: 0.6914 (mp0) REVERT: G 338 GLU cc_start: 0.7297 (tp30) cc_final: 0.6963 (tm-30) REVERT: G 346 PHE cc_start: 0.7748 (m-10) cc_final: 0.7433 (m-10) REVERT: G 353 LYS cc_start: 0.7790 (mtpp) cc_final: 0.7409 (ttpp) REVERT: G 357 LEU cc_start: 0.8867 (tt) cc_final: 0.8558 (tt) REVERT: I 346 PHE cc_start: 0.7762 (m-10) cc_final: 0.7235 (m-10) outliers start: 17 outliers final: 14 residues processed: 103 average time/residue: 0.4765 time to fit residues: 66.7322 Evaluate side-chains 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 371 ILE 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 325 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 356 SER 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 55 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4984 r_free = 0.4984 target = 0.177704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.128904 restraints weight = 19923.738| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 3.06 r_work: 0.4393 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.4285 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.7657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5660 Z= 0.138 Angle : 0.559 4.726 7580 Z= 0.287 Chirality : 0.050 0.158 860 Planarity : 0.003 0.027 960 Dihedral : 6.515 57.715 744 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 1.88 % Allowed : 19.38 % Favored : 78.75 % 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: -5.11 (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 0.005 0.001 HIS C 330 PHE 0.013 0.001 PHE H 346 TYR 0.009 0.002 TYR A 310 ARG 0.002 0.000 ARG B 349 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5660) covalent geometry : angle 0.55851 ( 7580) ********************** 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 96 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.4634 (mmtt) REVERT: B 370 LYS cc_start: 0.8157 (tptm) cc_final: 0.7916 (tptt) REVERT: E 342 GLU cc_start: 0.7110 (mp0) cc_final: 0.6872 (mp0) REVERT: G 338 GLU cc_start: 0.7144 (tp30) cc_final: 0.6836 (tm-30) REVERT: G 346 PHE cc_start: 0.7601 (m-10) cc_final: 0.7308 (m-10) REVERT: G 353 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7205 (ttpp) REVERT: G 357 LEU cc_start: 0.8798 (tt) cc_final: 0.8476 (tt) REVERT: I 346 PHE cc_start: 0.7695 (m-10) cc_final: 0.7197 (m-10) REVERT: I 354 ILE cc_start: 0.7757 (mp) cc_final: 0.7236 (tp) REVERT: J 354 ILE cc_start: 0.7332 (mm) cc_final: 0.7059 (tp) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.3878 time to fit residues: 47.8206 Evaluate side-chains 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 331 LYS Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 325 LEU 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 32 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.170948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.123130 restraints weight = 20532.935| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 3.01 r_work: 0.4300 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4192 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.7930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5660 Z= 0.252 Angle : 0.638 5.119 7580 Z= 0.332 Chirality : 0.051 0.142 860 Planarity : 0.004 0.027 960 Dihedral : 6.853 50.724 744 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.73 % Favored : 81.27 % Rotamer: Outliers : 2.19 % Allowed : 19.53 % Favored : 78.28 % 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 (0.20), 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 0.008 0.002 HIS C 374 PHE 0.018 0.002 PHE A 346 TYR 0.011 0.003 TYR A 310 ARG 0.002 0.000 ARG D 349 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 5660) covalent geometry : angle 0.63798 ( 7580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6637.72 seconds wall clock time: 117 minutes 51.86 seconds (7071.86 seconds total)