Starting phenix.real_space_refine on Tue Mar 3 11:38:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j6k_0690/03_2026/6j6k_0690.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j6k_0690/03_2026/6j6k_0690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6j6k_0690/03_2026/6j6k_0690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j6k_0690/03_2026/6j6k_0690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j6k_0690/03_2026/6j6k_0690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j6k_0690/03_2026/6j6k_0690.map" } resolution = 3.3 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= 0.001 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: 3 Type Number sf(0) Gaussians C 2224 2.51 5 N 620 2.21 5 O 704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3548 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 0.61, per 1000 atoms: 0.17 Number of scatterers: 3548 At special positions: 0 Unit cell: (70.551, 64.233, 66.339, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 704 8.00 N 620 7.00 C 2224 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: 0.27 Conformation dependent library (CDL) restraints added in 133.2 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.189A pdb=" N GLY A 41 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 56 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 108 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.189A pdb=" N GLY B 41 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 56 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP B 108 " --> pdb=" O GLY B 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.189A pdb=" N GLY C 41 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 56 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP C 108 " --> pdb=" O GLY C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 21 removed outlier: 4.188A pdb=" N GLY D 41 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 56 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP D 108 " --> pdb=" O GLY D 126 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 408 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: 0.54 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 572 1.29 - 1.36: 584 1.36 - 1.42: 480 1.42 - 1.49: 623 1.49 - 1.55: 1377 Bond restraints: 3636 Sorted by residual: bond pdb=" N ALA A 50 " pdb=" CA ALA A 50 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.31e+00 bond pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.24e+00 bond pdb=" N ALA C 50 " pdb=" CA ALA C 50 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.20e+00 bond pdb=" N ALA D 50 " pdb=" CA ALA D 50 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.20e+00 bond pdb=" C GLU C 44 " pdb=" N SER C 45 " ideal model delta sigma weight residual 1.332 1.352 -0.019 1.40e-02 5.10e+03 1.93e+00 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 4760 2.43 - 4.86: 160 4.86 - 7.29: 36 7.29 - 9.72: 8 9.72 - 12.15: 12 Bond angle restraints: 4976 Sorted by residual: angle pdb=" C SER C 45 " pdb=" N ALA C 46 " pdb=" CA ALA C 46 " ideal model delta sigma weight residual 121.54 133.69 -12.15 1.91e+00 2.74e-01 4.05e+01 angle pdb=" C SER D 45 " pdb=" N ALA D 46 " pdb=" CA ALA D 46 " ideal model delta sigma weight residual 121.54 133.68 -12.14 1.91e+00 2.74e-01 4.04e+01 angle pdb=" C SER B 45 " pdb=" N ALA B 46 " pdb=" CA ALA B 46 " ideal model delta sigma weight residual 121.54 133.68 -12.14 1.91e+00 2.74e-01 4.04e+01 angle pdb=" C SER A 45 " pdb=" N ALA A 46 " pdb=" CA ALA A 46 " ideal model delta sigma weight residual 121.54 133.67 -12.13 1.91e+00 2.74e-01 4.03e+01 angle pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 121.97 133.33 -11.36 1.80e+00 3.09e-01 3.98e+01 ... (remaining 4971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 1860 16.16 - 32.33: 84 32.33 - 48.49: 28 48.49 - 64.65: 4 64.65 - 80.82: 8 Dihedral angle restraints: 1984 sinusoidal: 664 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ALA B 46 " pdb=" C ALA B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual -180.00 -99.18 -80.82 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA ALA C 46 " pdb=" C ALA C 46 " pdb=" N VAL C 47 " pdb=" CA VAL C 47 " ideal model delta harmonic sigma weight residual -180.00 -99.21 -80.79 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA ALA A 46 " pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta harmonic sigma weight residual 180.00 -99.24 -80.76 0 5.00e+00 4.00e-02 2.61e+02 ... (remaining 1981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 356 0.042 - 0.084: 120 0.084 - 0.127: 52 0.127 - 0.169: 20 0.169 - 0.211: 8 Chirality restraints: 556 Sorted by residual: chirality pdb=" CA SER C 45 " pdb=" N SER C 45 " pdb=" C SER C 45 " pdb=" CB SER C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA SER D 45 " pdb=" N SER D 45 " pdb=" C SER D 45 " pdb=" CB SER D 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA SER A 45 " pdb=" N SER A 45 " pdb=" C SER A 45 " pdb=" CB SER A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 553 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 45 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C SER C 45 " -0.037 2.00e-02 2.50e+03 pdb=" O SER C 45 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA C 46 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 45 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C SER A 45 " 0.037 2.00e-02 2.50e+03 pdb=" O SER A 45 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 46 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 45 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C SER B 45 " 0.037 2.00e-02 2.50e+03 pdb=" O SER B 45 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA B 46 " -0.012 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1208 2.87 - 3.37: 2786 3.37 - 3.88: 5801 3.88 - 4.39: 6526 4.39 - 4.90: 12029 Nonbonded interactions: 28350 Sorted by model distance: nonbonded pdb=" O GLY D 34 " pdb=" OH TYR D 60 " model vdw 2.357 3.040 nonbonded pdb=" O GLY A 34 " pdb=" OH TYR A 60 " model vdw 2.357 3.040 nonbonded pdb=" O GLY B 34 " pdb=" OH TYR B 60 " model vdw 2.357 3.040 nonbonded pdb=" O GLY C 34 " pdb=" OH TYR C 60 " model vdw 2.358 3.040 nonbonded pdb=" NE1 TRP D 79 " pdb=" OG1 THR D 90 " model vdw 2.390 3.120 ... (remaining 28345 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' } 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.410 Find NCS groups from input model: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3636 Z= 0.247 Angle : 1.220 12.150 4976 Z= 0.681 Chirality : 0.058 0.211 556 Planarity : 0.004 0.022 624 Dihedral : 12.694 80.818 1160 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 2.56 % Allowed : 6.84 % Favored : 90.60 % Rotamer: Outliers : 1.16 % Allowed : 10.47 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % 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: -4.75 (0.27), residues: 468 helix: None (None), residues: 0 sheet: -2.62 (0.25), residues: 264 loop : -3.78 (0.24), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.014 0.002 TYR A 60 PHE 0.014 0.003 PHE A 29 TRP 0.017 0.003 TRP A 79 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 3636) covalent geometry : angle 1.22050 ( 4976) hydrogen bonds : bond 0.28715 ( 160) hydrogen bonds : angle 9.95450 ( 408) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.124 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 85 average time/residue: 0.0728 time to fit residues: 7.4262 Evaluate side-chains 46 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 118 ASN B 85 ASN B 118 ASN C 82 ASN C 85 ASN D 82 ASN D 85 ASN D 118 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.163822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129504 restraints weight = 4437.102| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.35 r_work: 0.3519 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3636 Z= 0.208 Angle : 0.829 6.872 4976 Z= 0.455 Chirality : 0.046 0.154 556 Planarity : 0.004 0.021 624 Dihedral : 8.837 69.077 512 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 1.71 % Allowed : 6.62 % Favored : 91.67 % Rotamer: Outliers : 5.23 % Allowed : 9.30 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -3.64 (0.31), residues: 468 helix: None (None), residues: 0 sheet: -1.86 (0.27), residues: 288 loop : -3.17 (0.28), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.007 0.001 TYR D 54 PHE 0.009 0.003 PHE D 29 TRP 0.012 0.002 TRP C 79 HIS 0.002 0.000 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 3636) covalent geometry : angle 0.82911 ( 4976) hydrogen bonds : bond 0.04739 ( 160) hydrogen bonds : angle 6.95567 ( 408) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.118 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 75 average time/residue: 0.0340 time to fit residues: 3.6733 Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.166634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133184 restraints weight = 4336.224| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.31 r_work: 0.3577 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3636 Z= 0.126 Angle : 0.731 6.407 4976 Z= 0.396 Chirality : 0.043 0.152 556 Planarity : 0.003 0.020 624 Dihedral : 7.830 59.701 512 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 1.71 % Allowed : 5.56 % Favored : 92.74 % Rotamer: Outliers : 4.07 % Allowed : 14.53 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -3.42 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.74 (0.27), residues: 296 loop : -2.99 (0.28), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.006 0.001 TYR A 43 PHE 0.009 0.001 PHE B 29 TRP 0.009 0.001 TRP B 108 HIS 0.002 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3636) covalent geometry : angle 0.73055 ( 4976) hydrogen bonds : bond 0.03954 ( 160) hydrogen bonds : angle 6.37458 ( 408) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.130 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 75 average time/residue: 0.0281 time to fit residues: 3.2665 Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS C 87 HIS D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.168087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135752 restraints weight = 4310.377| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.21 r_work: 0.3593 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3636 Z= 0.129 Angle : 0.687 5.967 4976 Z= 0.373 Chirality : 0.043 0.146 556 Planarity : 0.003 0.017 624 Dihedral : 7.149 52.105 512 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.05 % Favored : 92.09 % Rotamer: Outliers : 5.52 % Allowed : 17.44 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -3.16 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.56 (0.28), residues: 288 loop : -2.83 (0.27), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 53 TYR 0.005 0.001 TYR A 43 PHE 0.007 0.002 PHE A 29 TRP 0.010 0.001 TRP C 75 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3636) covalent geometry : angle 0.68700 ( 4976) hydrogen bonds : bond 0.03693 ( 160) hydrogen bonds : angle 6.22610 ( 408) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.111 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 77 average time/residue: 0.0270 time to fit residues: 3.1771 Evaluate side-chains 78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 122 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS D 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.157589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124702 restraints weight = 4437.085| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.29 r_work: 0.3444 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3636 Z= 0.314 Angle : 0.810 6.401 4976 Z= 0.437 Chirality : 0.047 0.154 556 Planarity : 0.003 0.015 624 Dihedral : 7.227 40.789 512 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 7.85 % Allowed : 17.73 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -3.05 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.46 (0.28), residues: 284 loop : -2.80 (0.29), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 103 TYR 0.008 0.002 TYR A 43 PHE 0.013 0.003 PHE C 130 TRP 0.013 0.002 TRP C 75 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 3636) covalent geometry : angle 0.80992 ( 4976) hydrogen bonds : bond 0.04297 ( 160) hydrogen bonds : angle 6.78762 ( 408) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.115 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 77 average time/residue: 0.0296 time to fit residues: 3.3158 Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 25 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS C 87 HIS D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130402 restraints weight = 4346.580| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.22 r_work: 0.3533 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3636 Z= 0.144 Angle : 0.709 5.485 4976 Z= 0.380 Chirality : 0.044 0.144 556 Planarity : 0.002 0.011 624 Dihedral : 6.232 29.339 512 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.85 % Allowed : 6.20 % Favored : 92.95 % Rotamer: Outliers : 5.81 % Allowed : 20.06 % Favored : 74.13 % 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: -2.82 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.34 (0.28), residues: 288 loop : -2.61 (0.29), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 53 TYR 0.007 0.001 TYR A 43 PHE 0.007 0.002 PHE C 29 TRP 0.011 0.001 TRP B 75 HIS 0.003 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3636) covalent geometry : angle 0.70890 ( 4976) hydrogen bonds : bond 0.03524 ( 160) hydrogen bonds : angle 6.30942 ( 408) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.088 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 71 average time/residue: 0.0363 time to fit residues: 3.6344 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS C 87 HIS D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119295 restraints weight = 4656.406| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.45 r_work: 0.3386 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3636 Z= 0.320 Angle : 0.799 6.338 4976 Z= 0.429 Chirality : 0.047 0.141 556 Planarity : 0.003 0.016 624 Dihedral : 6.599 24.564 512 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.76 % Favored : 90.38 % Rotamer: Outliers : 6.10 % Allowed : 21.80 % Favored : 72.09 % 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: -2.84 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.25 (0.28), residues: 280 loop : -2.79 (0.29), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.009 0.002 TYR B 43 PHE 0.010 0.003 PHE D 130 TRP 0.013 0.002 TRP A 75 HIS 0.002 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00712 ( 3636) covalent geometry : angle 0.79866 ( 4976) hydrogen bonds : bond 0.04199 ( 160) hydrogen bonds : angle 6.73553 ( 408) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.073 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 67 average time/residue: 0.0285 time to fit residues: 2.8750 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS C 87 HIS D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.164304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131254 restraints weight = 4310.468| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.28 r_work: 0.3502 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3636 Z= 0.133 Angle : 0.692 5.904 4976 Z= 0.369 Chirality : 0.043 0.131 556 Planarity : 0.002 0.015 624 Dihedral : 5.826 25.719 512 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 4.07 % Allowed : 23.84 % Favored : 72.09 % 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: -2.60 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.08 (0.28), residues: 280 loop : -2.64 (0.29), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.007 0.001 TYR B 43 PHE 0.007 0.002 PHE B 29 TRP 0.012 0.001 TRP C 108 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3636) covalent geometry : angle 0.69192 ( 4976) hydrogen bonds : bond 0.03400 ( 160) hydrogen bonds : angle 6.25840 ( 408) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.108 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 59 average time/residue: 0.0290 time to fit residues: 2.6146 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS C 87 HIS D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.166433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134052 restraints weight = 4185.248| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.23 r_work: 0.3541 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3636 Z= 0.124 Angle : 0.682 5.472 4976 Z= 0.363 Chirality : 0.042 0.128 556 Planarity : 0.003 0.016 624 Dihedral : 5.428 26.974 512 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 2.91 % Allowed : 26.16 % Favored : 70.93 % 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: -2.51 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -1.07 (0.28), residues: 284 loop : -2.51 (0.31), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 53 TYR 0.005 0.001 TYR B 43 PHE 0.008 0.002 PHE C 29 TRP 0.011 0.001 TRP A 108 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3636) covalent geometry : angle 0.68241 ( 4976) hydrogen bonds : bond 0.03341 ( 160) hydrogen bonds : angle 5.99067 ( 408) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.120 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.0422 time to fit residues: 3.6822 Evaluate side-chains 58 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS C 87 HIS D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.164981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131983 restraints weight = 4316.587| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.31 r_work: 0.3507 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3636 Z= 0.155 Angle : 0.697 5.476 4976 Z= 0.372 Chirality : 0.043 0.126 556 Planarity : 0.003 0.017 624 Dihedral : 5.552 29.310 512 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 2.62 % Allowed : 27.03 % Favored : 70.35 % 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: -2.39 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -0.96 (0.29), residues: 284 loop : -2.49 (0.32), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 53 TYR 0.006 0.001 TYR D 43 PHE 0.006 0.002 PHE B 29 TRP 0.012 0.001 TRP A 75 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3636) covalent geometry : angle 0.69662 ( 4976) hydrogen bonds : bond 0.03426 ( 160) hydrogen bonds : angle 6.13284 ( 408) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.070 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.0302 time to fit residues: 2.7415 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS C 87 HIS ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.161257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128013 restraints weight = 4265.419| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.32 r_work: 0.3448 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3636 Z= 0.230 Angle : 0.736 5.273 4976 Z= 0.395 Chirality : 0.044 0.131 556 Planarity : 0.003 0.019 624 Dihedral : 6.075 32.277 512 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.12 % Favored : 91.03 % Rotamer: Outliers : 2.91 % Allowed : 26.74 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -2.42 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -0.93 (0.28), residues: 280 loop : -2.59 (0.30), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.007 0.001 TYR A 43 PHE 0.009 0.002 PHE B 130 TRP 0.012 0.002 TRP C 75 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 3636) covalent geometry : angle 0.73598 ( 4976) hydrogen bonds : bond 0.03707 ( 160) hydrogen bonds : angle 6.48571 ( 408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 788.85 seconds wall clock time: 14 minutes 16.42 seconds (856.42 seconds total)