Starting phenix.real_space_refine on Tue Feb 3 12:20:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9li1_63109/02_2026/9li1_63109.cif Found real_map, /net/cci-nas-00/data/ceres_data/9li1_63109/02_2026/9li1_63109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9li1_63109/02_2026/9li1_63109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9li1_63109/02_2026/9li1_63109.map" model { file = "/net/cci-nas-00/data/ceres_data/9li1_63109/02_2026/9li1_63109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9li1_63109/02_2026/9li1_63109.cif" } resolution = 4.74 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= 0.001 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 6 5.16 5 C 1083 2.51 5 N 297 2.21 5 O 357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1743 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 581 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 0.41, per 1000 atoms: 0.24 Number of scatterers: 1743 At special positions: 0 Unit cell: (79.8, 79.8, 31.92, 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 6 16.00 O 357 8.00 N 297 7.00 C 1083 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: 0.14 Conformation dependent library (CDL) restraints added in 71.2 milliseconds 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 removed outlier: 6.164A pdb=" N ALA A 4 " --> pdb=" O VAL C 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 5.850A pdb=" N LEU A 8 " --> pdb=" O LYS B 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 15 removed outlier: 7.060A pdb=" N VAL A 14 " --> pdb=" O GLN B 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 33 removed outlier: 5.753A pdb=" N LYS A 30 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLY B 33 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP A 32 " --> pdb=" O GLY B 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 40 removed outlier: 8.156A pdb=" N SER C 34 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY A 33 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N LYS C 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 35 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.920A pdb=" N SER A 98 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 120 removed outlier: 6.323A pdb=" N VAL A 119 " --> pdb=" O HIS C 120 " (cutoff:3.500A) 13 hydrogen bonds defined for protein. 39 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.13 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 338 1.32 - 1.44: 361 1.44 - 1.56: 1053 1.56 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 1758 Sorted by residual: bond pdb=" CB VAL B 31 " pdb=" CG1 VAL B 31 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.22e+00 bond pdb=" CB VAL C 31 " pdb=" CG1 VAL C 31 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.20e+00 bond pdb=" CB VAL A 31 " pdb=" CG1 VAL A 31 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.15e+00 bond pdb=" CB VAL A 94 " pdb=" CG2 VAL A 94 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 4.98e+00 bond pdb=" CB VAL B 94 " pdb=" CG2 VAL B 94 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.88e+00 ... (remaining 1753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 2180 2.01 - 4.02: 130 4.02 - 6.04: 45 6.04 - 8.05: 15 8.05 - 10.06: 6 Bond angle restraints: 2376 Sorted by residual: angle pdb=" CA LYS C 23 " pdb=" CB LYS C 23 " pdb=" CG LYS C 23 " ideal model delta sigma weight residual 114.10 122.64 -8.54 2.00e+00 2.50e-01 1.82e+01 angle pdb=" CA LYS A 23 " pdb=" CB LYS A 23 " pdb=" CG LYS A 23 " ideal model delta sigma weight residual 114.10 122.64 -8.54 2.00e+00 2.50e-01 1.82e+01 angle pdb=" CA LYS B 23 " pdb=" CB LYS B 23 " pdb=" CG LYS B 23 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" N VAL B 94 " pdb=" CA VAL B 94 " pdb=" C VAL B 94 " ideal model delta sigma weight residual 107.77 101.92 5.85 1.48e+00 4.57e-01 1.56e+01 angle pdb=" N VAL A 94 " pdb=" CA VAL A 94 " pdb=" C VAL A 94 " ideal model delta sigma weight residual 107.77 101.92 5.85 1.48e+00 4.57e-01 1.56e+01 ... (remaining 2371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.88: 891 11.88 - 23.77: 108 23.77 - 35.65: 39 35.65 - 47.53: 6 47.53 - 59.41: 3 Dihedral angle restraints: 1047 sinusoidal: 393 harmonic: 654 Sorted by residual: dihedral pdb=" CA ALA C 93 " pdb=" C ALA C 93 " pdb=" N VAL C 94 " pdb=" CA VAL C 94 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ALA B 93 " pdb=" C ALA B 93 " pdb=" N VAL B 94 " pdb=" CA VAL B 94 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ALA A 93 " pdb=" C ALA A 93 " pdb=" N VAL A 94 " pdb=" CA VAL A 94 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 1044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 264 0.176 - 0.352: 18 0.352 - 0.527: 6 0.527 - 0.703: 0 0.703 - 0.879: 3 Chirality restraints: 291 Sorted by residual: chirality pdb=" CB ILE B 18 " pdb=" CA ILE B 18 " pdb=" CG1 ILE B 18 " pdb=" CG2 ILE B 18 " both_signs ideal model delta sigma weight residual False 2.64 1.77 0.88 2.00e-01 2.50e+01 1.93e+01 chirality pdb=" CB ILE C 18 " pdb=" CA ILE C 18 " pdb=" CG1 ILE C 18 " pdb=" CG2 ILE C 18 " both_signs ideal model delta sigma weight residual False 2.64 1.77 0.88 2.00e-01 2.50e+01 1.93e+01 chirality pdb=" CB ILE A 18 " pdb=" CA ILE A 18 " pdb=" CG1 ILE A 18 " pdb=" CG2 ILE A 18 " both_signs ideal model delta sigma weight residual False 2.64 1.77 0.88 2.00e-01 2.50e+01 1.92e+01 ... (remaining 288 not shown) Planarity restraints: 306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 86 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C ASN B 86 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN B 86 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 87 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 86 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ASN C 86 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN C 86 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL C 87 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 86 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ASN A 86 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN A 86 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 87 " 0.011 2.00e-02 2.50e+03 ... (remaining 303 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 944 2.96 - 3.44: 1778 3.44 - 3.93: 2739 3.93 - 4.41: 2921 4.41 - 4.90: 5670 Nonbonded interactions: 14052 Sorted by model distance: nonbonded pdb=" O ASP A 96 " pdb=" OD1 ASP B 96 " model vdw 2.472 3.040 nonbonded pdb=" O SER A 25 " pdb=" N ASN B 26 " model vdw 2.499 3.120 nonbonded pdb=" O LYS A 91 " pdb=" N ASP B 92 " model vdw 2.526 3.120 nonbonded pdb=" N LEU A 84 " pdb=" O ASP C 83 " model vdw 2.534 3.120 nonbonded pdb=" CG GLN A 22 " pdb=" OE1 GLN C 22 " model vdw 2.545 3.440 ... (remaining 14047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.320 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 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 : 0.008 0.075 1758 Z= 0.319 Angle : 1.412 10.061 2376 Z= 0.763 Chirality : 0.134 0.879 291 Planarity : 0.005 0.030 306 Dihedral : 12.236 59.413 627 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 36.59 Ramachandran Plot: Outliers : 1.32 % Allowed : 11.84 % Favored : 86.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.21 (0.46), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 115 PHE 0.013 0.005 PHE C 20 TRP 0.007 0.002 TRP A 32 HIS 0.001 0.000 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00802 ( 1758) covalent geometry : angle 1.41247 ( 2376) hydrogen bonds : bond 0.21022 ( 13) hydrogen bonds : angle 10.92560 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.020 Fit side-chains REVERT: A 9 LYS cc_start: 0.8599 (tttp) cc_final: 0.8222 (ttmt) REVERT: A 20 PHE cc_start: 0.6806 (p90) cc_final: 0.6350 (p90) REVERT: A 32 TRP cc_start: 0.5534 (t60) cc_final: 0.4400 (t60) REVERT: A 100 GLU cc_start: 0.8348 (pm20) cc_final: 0.6564 (mm-30) REVERT: A 101 ASP cc_start: 0.8003 (m-30) cc_final: 0.7004 (p0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0750 time to fit residues: 1.5972 Evaluate side-chains 11 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 0.0170 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087559 restraints weight = 1451.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.090015 restraints weight = 786.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091852 restraints weight = 513.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093207 restraints weight = 372.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094205 restraints weight = 288.392| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 1758 Z= 0.337 Angle : 1.130 8.555 2376 Z= 0.593 Chirality : 0.082 0.285 291 Planarity : 0.005 0.022 306 Dihedral : 8.378 35.420 237 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 34.88 Ramachandran Plot: Outliers : 1.32 % Allowed : 10.53 % Favored : 88.16 % Rotamer: Outliers : 7.69 % Allowed : 10.77 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.32 % 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: -3.87 (0.43), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.33), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.002 ARG A 115 PHE 0.023 0.007 PHE B 20 TRP 0.012 0.003 TRP A 32 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00794 ( 1758) covalent geometry : angle 1.13001 ( 2376) hydrogen bonds : bond 0.15233 ( 13) hydrogen bonds : angle 9.43386 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.023 Fit side-chains REVERT: A 3 LYS cc_start: 0.8007 (tmmt) cc_final: 0.7614 (pptt) REVERT: A 9 LYS cc_start: 0.8514 (tttp) cc_final: 0.8263 (ttmt) REVERT: A 100 GLU cc_start: 0.8536 (pm20) cc_final: 0.7113 (mm-30) REVERT: A 101 ASP cc_start: 0.7544 (m-30) cc_final: 0.7322 (m-30) outliers start: 5 outliers final: 0 residues processed: 20 average time/residue: 0.0440 time to fit residues: 0.9648 Evaluate side-chains 13 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.103701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089989 restraints weight = 1400.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.092263 restraints weight = 764.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093682 restraints weight = 492.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094792 restraints weight = 356.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095578 restraints weight = 278.243| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 1758 Z= 0.199 Angle : 0.890 7.328 2376 Z= 0.472 Chirality : 0.074 0.277 291 Planarity : 0.004 0.017 306 Dihedral : 6.632 17.063 237 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 28.02 Ramachandran Plot: Outliers : 1.32 % Allowed : 7.89 % Favored : 90.79 % Rotamer: Outliers : 1.54 % Allowed : 10.77 % Favored : 87.69 % 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: -3.36 (0.48), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 115 PHE 0.004 0.002 PHE A 20 TRP 0.009 0.002 TRP C 32 HIS 0.001 0.000 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 1758) covalent geometry : angle 0.89037 ( 2376) hydrogen bonds : bond 0.11185 ( 13) hydrogen bonds : angle 8.21427 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 304 Ramachandran restraints generated. 152 Oldfield, 0 Emsley, 152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 304 Ramachandran restraints generated. 152 Oldfield, 0 Emsley, 152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.016 Fit side-chains revert: symmetry clash REVERT: C 9 LYS cc_start: 0.8430 (tttp) cc_final: 0.7893 (ttmm) REVERT: C 17 ILE cc_start: 0.4606 (OUTLIER) cc_final: 0.4137 (pt) REVERT: C 26 ASN cc_start: 0.8681 (m-40) cc_final: 0.7215 (t0) REVERT: C 86 ASN cc_start: 0.6344 (p0) cc_final: 0.6038 (p0) REVERT: C 100 GLU cc_start: 0.8369 (pm20) cc_final: 0.7146 (mm-30) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0468 time to fit residues: 1.3603 Evaluate side-chains 20 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.0370 chunk 19 optimal weight: 0.0370 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.0000 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.104283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.090517 restraints weight = 1492.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093235 restraints weight = 746.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094620 restraints weight = 465.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.096116 restraints weight = 347.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097020 restraints weight = 266.075| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 1758 Z= 0.208 Angle : 0.964 7.063 2376 Z= 0.510 Chirality : 0.081 0.314 291 Planarity : 0.004 0.021 306 Dihedral : 7.283 26.159 237 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 35.73 Ramachandran Plot: Outliers : 2.63 % Allowed : 11.84 % Favored : 85.53 % Rotamer: Outliers : 1.54 % Allowed : 13.85 % Favored : 84.62 % 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: -3.82 (0.44), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 115 PHE 0.029 0.009 PHE C 20 TRP 0.006 0.001 TRP B 32 HIS 0.001 0.000 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 1758) covalent geometry : angle 0.96446 ( 2376) hydrogen bonds : bond 0.09521 ( 13) hydrogen bonds : angle 7.69052 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.025 Fit side-chains REVERT: B 25 SER cc_start: 0.8747 (p) cc_final: 0.7881 (p) REVERT: B 26 ASN cc_start: 0.9157 (m-40) cc_final: 0.7896 (t0) REVERT: B 100 GLU cc_start: 0.8102 (pm20) cc_final: 0.6712 (mm-30) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.0380 time to fit residues: 1.2579 Evaluate side-chains 13 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 7.9990 chunk 21 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 0.0970 chunk 5 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.087786 restraints weight = 1563.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.090504 restraints weight = 748.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092366 restraints weight = 450.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093595 restraints weight = 307.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094475 restraints weight = 233.096| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 1758 Z= 0.243 Angle : 1.070 8.096 2376 Z= 0.546 Chirality : 0.084 0.377 291 Planarity : 0.004 0.028 306 Dihedral : 8.690 33.586 237 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 33.73 Ramachandran Plot: Outliers : 1.32 % Allowed : 15.79 % Favored : 82.89 % Rotamer: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.32 % 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: -4.17 (0.44), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.33), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 115 PHE 0.004 0.001 PHE A 20 TRP 0.006 0.001 TRP C 32 HIS 0.009 0.003 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00675 ( 1758) covalent geometry : angle 1.07024 ( 2376) hydrogen bonds : bond 0.08625 ( 13) hydrogen bonds : angle 7.55979 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.026 Fit side-chains REVERT: A 9 LYS cc_start: 0.8628 (tttp) cc_final: 0.8398 (ttmt) REVERT: A 86 ASN cc_start: 0.7358 (t0) cc_final: 0.7093 (p0) REVERT: A 100 GLU cc_start: 0.8469 (pm20) cc_final: 0.7669 (tp30) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0560 time to fit residues: 1.2121 Evaluate side-chains 13 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.0010 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.086374 restraints weight = 1469.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.088949 restraints weight = 736.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.090871 restraints weight = 443.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.092149 restraints weight = 298.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092714 restraints weight = 219.589| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 1758 Z= 0.224 Angle : 1.069 9.035 2376 Z= 0.551 Chirality : 0.084 0.409 291 Planarity : 0.005 0.025 306 Dihedral : 8.155 32.159 237 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 32.59 Ramachandran Plot: Outliers : 2.63 % Allowed : 17.11 % Favored : 80.26 % Rotamer: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.63 % 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: -4.61 (0.44), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.33), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG B 115 PHE 0.043 0.013 PHE A 20 TRP 0.006 0.001 TRP C 32 HIS 0.006 0.002 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 1758) covalent geometry : angle 1.06865 ( 2376) hydrogen bonds : bond 0.08436 ( 13) hydrogen bonds : angle 7.59056 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.027 Fit side-chains REVERT: A 9 LYS cc_start: 0.8609 (tttp) cc_final: 0.8402 (ttmt) REVERT: A 22 GLN cc_start: 0.7476 (tp-100) cc_final: 0.7264 (tp-100) REVERT: A 23 LYS cc_start: 0.6528 (pptt) cc_final: 0.6094 (tppt) REVERT: A 25 SER cc_start: 0.8187 (p) cc_final: 0.7843 (p) REVERT: A 100 GLU cc_start: 0.8384 (pm20) cc_final: 0.7822 (tp30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0545 time to fit residues: 1.1165 Evaluate side-chains 13 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 0.0670 chunk 2 optimal weight: 0.0770 chunk 18 optimal weight: 0.0770 chunk 13 optimal weight: 0.0980 chunk 3 optimal weight: 0.0670 chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 19 optimal weight: 0.0670 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.0710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.103343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091736 restraints weight = 1470.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093696 restraints weight = 811.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095323 restraints weight = 532.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096276 restraints weight = 376.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097104 restraints weight = 292.858| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 1758 Z= 0.229 Angle : 1.106 8.866 2376 Z= 0.568 Chirality : 0.095 0.563 291 Planarity : 0.005 0.024 306 Dihedral : 8.049 36.914 237 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 33.45 Ramachandran Plot: Outliers : 1.32 % Allowed : 18.42 % Favored : 80.26 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.32 % 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: -4.85 (0.41), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.31), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 115 PHE 0.036 0.015 PHE C 20 TRP 0.005 0.001 TRP A 32 HIS 0.005 0.002 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 1758) covalent geometry : angle 1.10612 ( 2376) hydrogen bonds : bond 0.06655 ( 13) hydrogen bonds : angle 6.89524 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.024 Fit side-chains REVERT: A 23 LYS cc_start: 0.6275 (pptt) cc_final: 0.5632 (tppt) REVERT: A 25 SER cc_start: 0.8416 (p) cc_final: 0.7878 (t) REVERT: A 100 GLU cc_start: 0.8195 (pm20) cc_final: 0.7767 (mm-30) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0522 time to fit residues: 1.2978 Evaluate side-chains 13 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.0070 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082797 restraints weight = 1633.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084711 restraints weight = 966.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.086144 restraints weight = 661.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087152 restraints weight = 502.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.087870 restraints weight = 409.178| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 1758 Z= 0.390 Angle : 1.320 10.138 2376 Z= 0.687 Chirality : 0.110 0.670 291 Planarity : 0.005 0.025 306 Dihedral : 10.167 48.732 237 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 42.88 Ramachandran Plot: Outliers : 2.63 % Allowed : 21.05 % Favored : 76.32 % Rotamer: Outliers : 1.54 % Allowed : 6.15 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.63 % 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: -4.58 (0.45), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 115 PHE 0.023 0.010 PHE A 20 TRP 0.008 0.002 TRP A 32 HIS 0.005 0.002 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.01026 ( 1758) covalent geometry : angle 1.32048 ( 2376) hydrogen bonds : bond 0.10826 ( 13) hydrogen bonds : angle 8.18818 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.026 Fit side-chains REVERT: C 3 LYS cc_start: 0.8141 (tmmt) cc_final: 0.7508 (pptt) REVERT: C 17 ILE cc_start: 0.5850 (mm) cc_final: 0.5550 (pt) REVERT: C 26 ASN cc_start: 0.9125 (m-40) cc_final: 0.7829 (t0) REVERT: C 115 ARG cc_start: 0.7868 (mmm-85) cc_final: 0.5570 (mtm180) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0638 time to fit residues: 1.4320 Evaluate side-chains 12 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.0570 chunk 8 optimal weight: 10.0000 chunk 10 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 overall best weight: 0.6936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086960 restraints weight = 1348.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089383 restraints weight = 746.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091140 restraints weight = 492.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092534 restraints weight = 359.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093417 restraints weight = 279.608| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 1758 Z= 0.249 Angle : 1.227 11.211 2376 Z= 0.634 Chirality : 0.097 0.395 291 Planarity : 0.005 0.036 306 Dihedral : 9.460 33.928 237 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 36.02 Ramachandran Plot: Outliers : 1.32 % Allowed : 22.37 % Favored : 76.32 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.63 % 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: -4.50 (0.45), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 115 PHE 0.018 0.008 PHE B 20 TRP 0.009 0.002 TRP A 32 HIS 0.003 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 1758) covalent geometry : angle 1.22724 ( 2376) hydrogen bonds : bond 0.05349 ( 13) hydrogen bonds : angle 6.26495 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.015 Fit side-chains REVERT: A 3 LYS cc_start: 0.7366 (tmmt) cc_final: 0.6925 (pptt) REVERT: A 112 ILE cc_start: 0.8977 (mm) cc_final: 0.8726 (mm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0373 time to fit residues: 0.7844 Evaluate side-chains 10 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.0370 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 0.0470 chunk 21 optimal weight: 0.0020 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 0.0020 chunk 10 optimal weight: 0.0370 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 0.0470 chunk 15 optimal weight: 0.0470 chunk 4 optimal weight: 9.9990 overall best weight: 0.0250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094171 restraints weight = 1472.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.096869 restraints weight = 834.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098798 restraints weight = 547.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099966 restraints weight = 395.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.101151 restraints weight = 314.480| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 1758 Z= 0.310 Angle : 1.542 14.114 2376 Z= 0.791 Chirality : 0.153 0.946 291 Planarity : 0.006 0.038 306 Dihedral : 9.332 37.459 237 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 39.17 Ramachandran Plot: Outliers : 1.32 % Allowed : 17.11 % Favored : 81.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.32 % 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: -4.82 (0.39), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.30), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 115 PHE 0.014 0.006 PHE C 20 TRP 0.008 0.002 TRP A 32 HIS 0.003 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00809 ( 1758) covalent geometry : angle 1.54200 ( 2376) hydrogen bonds : bond 0.10082 ( 13) hydrogen bonds : angle 8.15772 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 152 Ramachandran restraints generated. 76 Oldfield, 0 Emsley, 76 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.014 Fit side-chains REVERT: C 88 THR cc_start: 0.7453 (p) cc_final: 0.7043 (t) REVERT: C 90 ASP cc_start: 0.7358 (p0) cc_final: 0.7064 (p0) REVERT: C 92 ASP cc_start: 0.6656 (m-30) cc_final: 0.6143 (p0) REVERT: C 100 GLU cc_start: 0.7964 (pm20) cc_final: 0.6911 (mm-30) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0221 time to fit residues: 0.4996 Evaluate side-chains 13 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.091661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080172 restraints weight = 1763.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.081964 restraints weight = 946.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083384 restraints weight = 612.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084409 restraints weight = 434.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085071 restraints weight = 331.087| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.099 1758 Z= 0.488 Angle : 1.612 11.504 2376 Z= 0.840 Chirality : 0.143 1.104 291 Planarity : 0.009 0.069 306 Dihedral : 12.609 54.889 237 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 56.89 Ramachandran Plot: Outliers : 2.63 % Allowed : 19.74 % Favored : 77.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 1.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.95 % 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: -4.14 (0.44), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 115 PHE 0.026 0.012 PHE B 20 TRP 0.010 0.002 TRP A 32 HIS 0.004 0.002 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.01287 ( 1758) covalent geometry : angle 1.61247 ( 2376) hydrogen bonds : bond 0.11935 ( 13) hydrogen bonds : angle 8.59263 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 495.26 seconds wall clock time: 9 minutes 8.22 seconds (548.22 seconds total)