Starting phenix.real_space_refine on Sat May 2 06:46:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9riv_54006/05_2026/9riv_54006.cif Found real_map, /net/cci-nas-00/data/ceres_data/9riv_54006/05_2026/9riv_54006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9riv_54006/05_2026/9riv_54006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9riv_54006/05_2026/9riv_54006.map" model { file = "/net/cci-nas-00/data/ceres_data/9riv_54006/05_2026/9riv_54006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9riv_54006/05_2026/9riv_54006.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1940 2.51 5 N 530 2.21 5 O 570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3050 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "B" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "D" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "E" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "F" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "G" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "H" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "I" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "J" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Time building chain proxies: 0.94, per 1000 atoms: 0.31 Number of scatterers: 3050 At special positions: 0 Unit cell: (72.42, 60.35, 51.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 570 8.00 N 530 7.00 C 1940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 141.7 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 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: 0.49 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: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1040 1.34 - 1.46: 685 1.46 - 1.57: 1365 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 3110 Sorted by residual: bond pdb=" N ALA F 2 " pdb=" CA ALA F 2 " ideal model delta sigma weight residual 1.459 1.454 0.005 1.20e-02 6.94e+03 1.68e-01 bond pdb=" N ALA B 2 " pdb=" CA ALA B 2 " ideal model delta sigma weight residual 1.459 1.455 0.005 1.20e-02 6.94e+03 1.51e-01 bond pdb=" N ALA D 2 " pdb=" CA ALA D 2 " ideal model delta sigma weight residual 1.459 1.455 0.005 1.20e-02 6.94e+03 1.49e-01 bond pdb=" N ALA C 2 " pdb=" CA ALA C 2 " ideal model delta sigma weight residual 1.459 1.455 0.004 1.20e-02 6.94e+03 1.40e-01 bond pdb=" CB VAL C 39 " pdb=" CG1 VAL C 39 " ideal model delta sigma weight residual 1.521 1.509 0.012 3.30e-02 9.18e+02 1.28e-01 ... (remaining 3105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.48: 3620 0.48 - 0.96: 468 0.96 - 1.45: 62 1.45 - 1.93: 10 1.93 - 2.41: 10 Bond angle restraints: 4170 Sorted by residual: angle pdb=" N GLU F 11 " pdb=" CA GLU F 11 " pdb=" C GLU F 11 " ideal model delta sigma weight residual 107.93 109.16 -1.23 1.65e+00 3.67e-01 5.54e-01 angle pdb=" N GLU H 11 " pdb=" CA GLU H 11 " pdb=" C GLU H 11 " ideal model delta sigma weight residual 107.93 109.13 -1.20 1.65e+00 3.67e-01 5.25e-01 angle pdb=" N GLU C 11 " pdb=" CA GLU C 11 " pdb=" C GLU C 11 " ideal model delta sigma weight residual 107.93 109.11 -1.18 1.65e+00 3.67e-01 5.13e-01 angle pdb=" N GLU G 11 " pdb=" CA GLU G 11 " pdb=" C GLU G 11 " ideal model delta sigma weight residual 107.93 109.10 -1.17 1.65e+00 3.67e-01 5.07e-01 angle pdb=" N GLU J 11 " pdb=" CA GLU J 11 " pdb=" C GLU J 11 " ideal model delta sigma weight residual 107.93 109.10 -1.17 1.65e+00 3.67e-01 5.06e-01 ... (remaining 4165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.11: 1507 10.11 - 20.21: 143 20.21 - 30.31: 70 30.31 - 40.42: 10 40.42 - 50.52: 10 Dihedral angle restraints: 1740 sinusoidal: 660 harmonic: 1080 Sorted by residual: dihedral pdb=" CA LEU J 34 " pdb=" CB LEU J 34 " pdb=" CG LEU J 34 " pdb=" CD1 LEU J 34 " ideal model delta sinusoidal sigma weight residual 180.00 141.53 38.47 3 1.50e+01 4.44e-03 6.78e+00 dihedral pdb=" CA LEU E 34 " pdb=" CB LEU E 34 " pdb=" CG LEU E 34 " pdb=" CD1 LEU E 34 " ideal model delta sinusoidal sigma weight residual 180.00 141.54 38.46 3 1.50e+01 4.44e-03 6.77e+00 dihedral pdb=" CA LEU C 34 " pdb=" CB LEU C 34 " pdb=" CG LEU C 34 " pdb=" CD1 LEU C 34 " ideal model delta sinusoidal sigma weight residual 180.00 141.56 38.44 3 1.50e+01 4.44e-03 6.77e+00 ... (remaining 1737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 200 0.027 - 0.053: 155 0.053 - 0.080: 25 0.080 - 0.106: 36 0.106 - 0.133: 24 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA ILE D 32 " pdb=" N ILE D 32 " pdb=" C ILE D 32 " pdb=" CB ILE D 32 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE C 32 " pdb=" N ILE C 32 " pdb=" C ILE C 32 " pdb=" CB ILE C 32 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE A 32 " pdb=" N ILE A 32 " pdb=" C ILE A 32 " pdb=" CB ILE A 32 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 437 not shown) Planarity restraints: 550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 7 " 0.002 2.00e-02 2.50e+03 3.48e-03 1.21e-01 pdb=" C ASP A 7 " -0.006 2.00e-02 2.50e+03 pdb=" O ASP A 7 " 0.002 2.00e-02 2.50e+03 pdb=" N SER A 8 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 19 " -0.003 2.00e-02 2.50e+03 2.56e-03 1.15e-01 pdb=" CG PHE F 19 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE F 19 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 19 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 7 " 0.002 2.00e-02 2.50e+03 3.35e-03 1.12e-01 pdb=" C ASP E 7 " -0.006 2.00e-02 2.50e+03 pdb=" O ASP E 7 " 0.002 2.00e-02 2.50e+03 pdb=" N SER E 8 " 0.002 2.00e-02 2.50e+03 ... (remaining 547 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 1961 3.10 - 3.55: 3055 3.55 - 4.00: 4687 4.00 - 4.45: 5426 4.45 - 4.90: 9567 Nonbonded interactions: 24696 Sorted by model distance: nonbonded pdb=" OD2 ASP E 1 " pdb=" OD2 ASP G 23 " model vdw 2.645 3.040 nonbonded pdb=" OD2 ASP D 1 " pdb=" OD2 ASP F 23 " model vdw 2.646 3.040 nonbonded pdb=" N SER B 8 " pdb=" O SER B 8 " model vdw 2.690 2.496 nonbonded pdb=" N SER I 8 " pdb=" O SER I 8 " model vdw 2.690 2.496 nonbonded pdb=" N SER C 8 " pdb=" O SER C 8 " model vdw 2.691 2.496 ... (remaining 24691 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: 0.01 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: 8.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:7.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 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 : 0.002 0.012 3110 Z= 0.108 Angle : 0.346 2.408 4170 Z= 0.191 Chirality : 0.049 0.133 440 Planarity : 0.001 0.003 550 Dihedral : 10.795 50.524 1060 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.37), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 5 TYR 0.002 0.000 TYR I 10 PHE 0.006 0.001 PHE F 19 HIS 0.002 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 3110) covalent geometry : angle 0.34625 ( 4170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.073 Fit side-chains REVERT: E 18 VAL cc_start: 0.9439 (m) cc_final: 0.9201 (t) REVERT: H 22 GLU cc_start: 0.8615 (tt0) cc_final: 0.8285 (tm-30) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.5995 time to fit residues: 81.4796 Evaluate side-chains 95 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.097839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.089869 restraints weight = 5042.711| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.10 r_work: 0.3269 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3110 Z= 0.179 Angle : 0.455 4.431 4170 Z= 0.234 Chirality : 0.050 0.125 440 Planarity : 0.002 0.006 550 Dihedral : 3.523 9.521 410 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 10.00 % Allowed : 23.87 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.37), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 5 TYR 0.003 0.001 TYR C 10 PHE 0.013 0.002 PHE G 19 HIS 0.001 0.000 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 3110) covalent geometry : angle 0.45460 ( 4170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.099 Fit side-chains REVERT: F 7 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8798 (m-30) REVERT: G 22 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: I 22 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8043 (tt0) outliers start: 31 outliers final: 8 residues processed: 101 average time/residue: 0.6748 time to fit residues: 69.5168 Evaluate side-chains 95 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.097611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089879 restraints weight = 5093.719| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.08 r_work: 0.3265 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3110 Z= 0.160 Angle : 0.425 4.029 4170 Z= 0.221 Chirality : 0.049 0.122 440 Planarity : 0.001 0.006 550 Dihedral : 3.441 8.982 410 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 9.35 % Allowed : 24.84 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.36), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG D 5 TYR 0.003 0.001 TYR F 10 PHE 0.010 0.002 PHE G 19 HIS 0.001 0.000 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3110) covalent geometry : angle 0.42498 ( 4170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.126 Fit side-chains REVERT: A 11 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8820 (tt0) REVERT: B 11 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8853 (tt0) REVERT: C 11 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8737 (tt0) REVERT: E 22 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: F 7 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8778 (m-30) REVERT: G 22 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: H 22 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: I 22 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8112 (tt0) outliers start: 29 outliers final: 13 residues processed: 99 average time/residue: 0.7233 time to fit residues: 72.9524 Evaluate side-chains 102 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.098928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091243 restraints weight = 5037.343| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.06 r_work: 0.3286 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3110 Z= 0.121 Angle : 0.400 3.680 4170 Z= 0.208 Chirality : 0.049 0.121 440 Planarity : 0.001 0.005 550 Dihedral : 3.302 8.234 410 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.71 % Allowed : 26.45 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.37), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 5 TYR 0.002 0.001 TYR F 10 PHE 0.009 0.001 PHE G 19 HIS 0.001 0.000 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3110) covalent geometry : angle 0.40038 ( 4170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.075 Fit side-chains REVERT: A 11 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8814 (tt0) REVERT: B 11 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8842 (tt0) REVERT: C 11 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8732 (tt0) REVERT: E 22 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: F 7 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8746 (m-30) REVERT: G 22 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: H 22 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: I 22 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8115 (tt0) outliers start: 27 outliers final: 9 residues processed: 93 average time/residue: 0.7421 time to fit residues: 70.2989 Evaluate side-chains 99 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.094647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087019 restraints weight = 5093.433| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.05 r_work: 0.3215 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3110 Z= 0.235 Angle : 0.522 7.124 4170 Z= 0.265 Chirality : 0.049 0.124 440 Planarity : 0.002 0.006 550 Dihedral : 3.772 9.168 410 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 11.29 % Allowed : 23.55 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.35), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 5 TYR 0.004 0.001 TYR J 10 PHE 0.011 0.002 PHE J 19 HIS 0.002 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 3110) covalent geometry : angle 0.52199 ( 4170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.091 Fit side-chains REVERT: A 11 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8820 (tt0) REVERT: B 11 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8832 (tt0) REVERT: B 22 GLU cc_start: 0.8909 (tt0) cc_final: 0.8696 (tt0) REVERT: C 11 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: D 1 ASP cc_start: 0.7589 (t0) cc_final: 0.7140 (t0) REVERT: E 17 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9216 (mt) REVERT: E 22 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: F 7 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8838 (m-30) REVERT: G 22 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: H 22 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: I 22 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8068 (tt0) outliers start: 35 outliers final: 15 residues processed: 105 average time/residue: 0.6475 time to fit residues: 69.3817 Evaluate side-chains 107 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.096739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089200 restraints weight = 5012.146| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.02 r_work: 0.3255 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3110 Z= 0.156 Angle : 0.442 4.432 4170 Z= 0.227 Chirality : 0.049 0.121 440 Planarity : 0.001 0.006 550 Dihedral : 3.546 8.858 410 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 10.65 % Allowed : 24.19 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.35), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 5 TYR 0.003 0.001 TYR F 10 PHE 0.011 0.002 PHE J 20 HIS 0.001 0.000 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3110) covalent geometry : angle 0.44192 ( 4170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.148 Fit side-chains REVERT: A 11 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8827 (tt0) REVERT: B 11 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8830 (tt0) REVERT: C 11 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8757 (tt0) REVERT: D 1 ASP cc_start: 0.7494 (t0) cc_final: 0.7075 (t0) REVERT: E 22 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: F 7 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8765 (m-30) REVERT: G 22 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: I 22 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8088 (tt0) outliers start: 33 outliers final: 14 residues processed: 104 average time/residue: 0.6304 time to fit residues: 66.9079 Evaluate side-chains 106 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 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 = 0.3411 r_free = 0.3411 target = 0.092843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.085522 restraints weight = 5227.818| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.05 r_work: 0.3195 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.046 3110 Z= 0.364 Angle : 0.614 5.383 4170 Z= 0.316 Chirality : 0.052 0.178 440 Planarity : 0.002 0.008 550 Dihedral : 4.123 9.835 410 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 12.26 % Allowed : 22.26 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 5 TYR 0.006 0.002 TYR J 10 PHE 0.014 0.002 PHE J 19 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00881 ( 3110) covalent geometry : angle 0.61368 ( 4170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.111 Fit side-chains REVERT: A 11 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8824 (tt0) REVERT: B 11 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8859 (tt0) REVERT: C 11 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8751 (tt0) REVERT: D 1 ASP cc_start: 0.7410 (t0) cc_final: 0.7025 (t0) REVERT: E 17 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9225 (mt) REVERT: E 22 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: F 7 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8881 (m-30) REVERT: G 22 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: I 22 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8133 (tt0) outliers start: 38 outliers final: 18 residues processed: 104 average time/residue: 0.6527 time to fit residues: 69.2120 Evaluate side-chains 108 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.096717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.089332 restraints weight = 5158.972| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.04 r_work: 0.3248 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3110 Z= 0.151 Angle : 0.468 5.720 4170 Z= 0.238 Chirality : 0.050 0.121 440 Planarity : 0.001 0.008 550 Dihedral : 3.652 9.312 410 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 8.39 % Allowed : 26.45 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 5 TYR 0.003 0.001 TYR J 10 PHE 0.012 0.002 PHE J 20 HIS 0.002 0.000 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3110) covalent geometry : angle 0.46782 ( 4170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.082 Fit side-chains REVERT: A 11 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8876 (tt0) REVERT: B 11 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8847 (tt0) REVERT: C 11 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: D 1 ASP cc_start: 0.7322 (t0) cc_final: 0.7093 (t0) REVERT: E 22 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: F 7 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8798 (m-30) REVERT: G 22 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: I 22 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8100 (tt0) outliers start: 26 outliers final: 13 residues processed: 100 average time/residue: 0.6718 time to fit residues: 68.4468 Evaluate side-chains 104 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.0040 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 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 = 0.3444 r_free = 0.3444 target = 0.095318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.087936 restraints weight = 5205.426| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.06 r_work: 0.3222 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3110 Z= 0.203 Angle : 0.522 7.364 4170 Z= 0.261 Chirality : 0.050 0.123 440 Planarity : 0.002 0.007 550 Dihedral : 3.777 9.105 410 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 9.03 % Allowed : 25.81 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.35), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 5 TYR 0.003 0.001 TYR J 10 PHE 0.016 0.002 PHE J 20 HIS 0.002 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 3110) covalent geometry : angle 0.52173 ( 4170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.103 Fit side-chains REVERT: A 11 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: B 11 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8854 (tt0) REVERT: C 11 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8804 (tt0) REVERT: D 1 ASP cc_start: 0.7355 (t0) cc_final: 0.7105 (t0) REVERT: E 22 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: F 7 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8842 (m-30) REVERT: G 22 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: I 22 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8088 (tt0) outliers start: 28 outliers final: 13 residues processed: 98 average time/residue: 0.6570 time to fit residues: 65.6155 Evaluate side-chains 104 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.097907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090573 restraints weight = 5027.366| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.01 r_work: 0.3285 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3110 Z= 0.116 Angle : 0.454 8.374 4170 Z= 0.226 Chirality : 0.050 0.124 440 Planarity : 0.001 0.008 550 Dihedral : 3.455 8.417 410 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.45 % Allowed : 28.39 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.35), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 5 TYR 0.002 0.001 TYR J 10 PHE 0.018 0.002 PHE J 20 HIS 0.001 0.000 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3110) covalent geometry : angle 0.45407 ( 4170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.098 Fit side-chains REVERT: A 11 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8840 (tt0) REVERT: B 11 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8834 (tt0) REVERT: C 11 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8754 (tt0) REVERT: D 1 ASP cc_start: 0.7324 (t0) cc_final: 0.7112 (t0) REVERT: E 22 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: F 7 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8729 (m-30) REVERT: G 22 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: I 22 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8108 (tt0) outliers start: 20 outliers final: 11 residues processed: 97 average time/residue: 0.6635 time to fit residues: 65.5824 Evaluate side-chains 104 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.098915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.091710 restraints weight = 5042.043| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.97 r_work: 0.3308 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3110 Z= 0.111 Angle : 0.448 7.692 4170 Z= 0.223 Chirality : 0.050 0.119 440 Planarity : 0.001 0.006 550 Dihedral : 3.394 8.164 410 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.16 % Allowed : 29.68 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.36), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 5 TYR 0.002 0.001 TYR J 10 PHE 0.011 0.002 PHE G 20 HIS 0.001 0.000 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3110) covalent geometry : angle 0.44778 ( 4170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.52 seconds wall clock time: 30 minutes 9.26 seconds (1809.26 seconds total)