Starting phenix.real_space_refine on Tue Feb 3 12:20:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9je4_61406/02_2026/9je4_61406.cif Found real_map, /net/cci-nas-00/data/ceres_data/9je4_61406/02_2026/9je4_61406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9je4_61406/02_2026/9je4_61406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9je4_61406/02_2026/9je4_61406.map" model { file = "/net/cci-nas-00/data/ceres_data/9je4_61406/02_2026/9je4_61406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9je4_61406/02_2026/9je4_61406.cif" } resolution = 3.37 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= 0.002 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 954 2.51 5 N 270 2.21 5 O 309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 1533 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 446 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Restraints were copied for chains: B, C, G, H Time building chain proxies: 0.45, per 1000 atoms: 0.29 Number of scatterers: 1533 At special positions: 0 Unit cell: (78.02, 67.23, 30.71, 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 309 8.00 N 270 7.00 C 954 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 63.6 milliseconds 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 414 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 58 removed outlier: 6.906A pdb=" N GLU A 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY C 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 52 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR C 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR A 54 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N THR C 54 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N THR B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N ALA C 56 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N LYS C 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA B 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 removed outlier: 6.436A pdb=" N THR A 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.418A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 78 removed outlier: 6.344A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA C 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.523A pdb=" N THR B 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.586A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.768A pdb=" N GLY A 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LYS C 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY C 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) 14 hydrogen bonds defined for protein. 42 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: 0.18 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 273 1.29 - 1.35: 246 1.35 - 1.42: 51 1.42 - 1.48: 258 1.48 - 1.55: 708 Bond restraints: 1536 Sorted by residual: bond pdb=" CA VAL A 37 " pdb=" CB VAL A 37 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.59e-01 bond pdb=" N LYS B 43 " pdb=" CA LYS B 43 " ideal model delta sigma weight residual 1.466 1.456 0.010 1.36e-02 5.41e+03 5.43e-01 bond pdb=" CA VAL C 37 " pdb=" CB VAL C 37 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.36e-01 bond pdb=" CA VAL B 37 " pdb=" CB VAL B 37 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.22e-01 bond pdb=" N LYS A 43 " pdb=" CA LYS A 43 " ideal model delta sigma weight residual 1.466 1.457 0.010 1.36e-02 5.41e+03 5.13e-01 ... (remaining 1531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.61: 1688 0.61 - 1.22: 285 1.22 - 1.83: 94 1.83 - 2.44: 12 2.44 - 3.05: 6 Bond angle restraints: 2085 Sorted by residual: angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 122.21 119.16 3.05 1.62e+00 3.81e-01 3.54e+00 angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 122.21 119.20 3.01 1.62e+00 3.81e-01 3.44e+00 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 122.21 119.21 3.00 1.62e+00 3.81e-01 3.43e+00 angle pdb=" N GLY A 41 " pdb=" CA GLY A 41 " pdb=" C GLY A 41 " ideal model delta sigma weight residual 112.81 110.66 2.15 1.38e+00 5.25e-01 2.42e+00 angle pdb=" CA LYS B 60 " pdb=" C LYS B 60 " pdb=" O LYS B 60 " ideal model delta sigma weight residual 122.41 120.53 1.88 1.21e+00 6.83e-01 2.41e+00 ... (remaining 2080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 833 17.84 - 35.68: 58 35.68 - 53.52: 6 53.52 - 71.36: 6 71.36 - 89.21: 3 Dihedral angle restraints: 906 sinusoidal: 264 harmonic: 642 Sorted by residual: dihedral pdb=" CA SER B 42 " pdb=" C SER B 42 " pdb=" N LYS B 43 " pdb=" CA LYS B 43 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA SER C 42 " pdb=" C SER C 42 " pdb=" N LYS C 43 " pdb=" CA LYS C 43 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA SER A 42 " pdb=" C SER A 42 " pdb=" N LYS A 43 " pdb=" CA LYS A 43 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 117 0.027 - 0.054: 87 0.054 - 0.081: 33 0.081 - 0.107: 25 0.107 - 0.134: 20 Chirality restraints: 282 Sorted by residual: chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 279 not shown) Planarity restraints: 261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.009 2.00e-02 2.50e+03 7.60e-03 8.65e-01 pdb=" CG HIS A 50 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.009 2.00e-02 2.50e+03 7.46e-03 8.34e-01 pdb=" CG HIS B 50 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " 0.009 2.00e-02 2.50e+03 7.33e-03 8.06e-01 pdb=" CG HIS C 50 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " 0.003 2.00e-02 2.50e+03 ... (remaining 258 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 295 2.79 - 3.31: 1355 3.31 - 3.84: 2324 3.84 - 4.37: 2511 4.37 - 4.90: 5182 Nonbonded interactions: 11667 Sorted by model distance: nonbonded pdb=" ND1 HIS B 50 " pdb=" OD2 ASP B 51 " model vdw 2.258 3.120 nonbonded pdb=" ND1 HIS C 50 " pdb=" OD2 ASP C 51 " model vdw 2.258 3.120 nonbonded pdb=" ND1 HIS A 50 " pdb=" OD2 ASP A 51 " model vdw 2.258 3.120 nonbonded pdb=" O THR C 59 " pdb=" OG1 THR C 59 " model vdw 2.322 3.040 nonbonded pdb=" O THR A 59 " pdb=" OG1 THR A 59 " model vdw 2.322 3.040 ... (remaining 11662 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' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.190 Find NCS groups from input model: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 : 0.003 0.020 1536 Z= 0.186 Angle : 0.556 3.049 2085 Z= 0.351 Chirality : 0.053 0.134 282 Planarity : 0.002 0.008 261 Dihedral : 15.196 89.206 492 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -3.52 (0.42), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.32), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.005 0.001 PHE A 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 1536) covalent geometry : angle 0.55582 ( 2085) hydrogen bonds : bond 0.16820 ( 14) hydrogen bonds : angle 8.33580 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.051 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0826 Evaluate side-chains 0 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.0000 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.139584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.117820 restraints weight = 1694.143| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.66 r_work: 0.4040 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1536 Z= 0.113 Angle : 0.442 3.262 2085 Z= 0.256 Chirality : 0.050 0.134 282 Planarity : 0.002 0.009 261 Dihedral : 4.995 16.808 228 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -2.66 (0.50), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 39 PHE 0.005 0.001 PHE C 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 1536) covalent geometry : angle 0.44172 ( 2085) hydrogen bonds : bond 0.01902 ( 14) hydrogen bonds : angle 6.15291 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0922 Evaluate side-chains 0 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.128691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.105660 restraints weight = 1806.512| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.83 r_work: 0.3828 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 1536 Z= 0.256 Angle : 0.630 7.082 2085 Z= 0.347 Chirality : 0.055 0.182 282 Planarity : 0.003 0.012 261 Dihedral : 5.924 21.002 228 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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: -2.57 (0.51), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR B 39 PHE 0.007 0.002 PHE C 94 HIS 0.009 0.006 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 1536) covalent geometry : angle 0.62956 ( 2085) hydrogen bonds : bond 0.02248 ( 14) hydrogen bonds : angle 5.70558 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0210 time to fit residues: 0.1668 Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.130946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.108473 restraints weight = 1808.488| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.79 r_work: 0.3736 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1536 Z= 0.178 Angle : 0.532 5.359 2085 Z= 0.297 Chirality : 0.052 0.143 282 Planarity : 0.002 0.012 261 Dihedral : 5.477 18.585 228 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.54), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.005 0.001 PHE A 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 1536) covalent geometry : angle 0.53151 ( 2085) hydrogen bonds : bond 0.01932 ( 14) hydrogen bonds : angle 5.52033 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.039 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0367 time to fit residues: 0.1543 Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.131153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.108693 restraints weight = 1774.008| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.85 r_work: 0.3910 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1536 Z= 0.158 Angle : 0.496 5.111 2085 Z= 0.278 Chirality : 0.051 0.142 282 Planarity : 0.002 0.011 261 Dihedral : 5.201 17.815 228 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % 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: -2.20 (0.55), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.005 0.001 PHE A 94 HIS 0.007 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 1536) covalent geometry : angle 0.49644 ( 2085) hydrogen bonds : bond 0.01783 ( 14) hydrogen bonds : angle 5.40431 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0279 time to fit residues: 0.1172 Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.123943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.101347 restraints weight = 1805.246| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.80 r_work: 0.3802 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 1536 Z= 0.277 Angle : 0.650 6.881 2085 Z= 0.356 Chirality : 0.056 0.181 282 Planarity : 0.003 0.012 261 Dihedral : 6.003 19.920 228 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.56), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR B 39 PHE 0.007 0.002 PHE C 94 HIS 0.010 0.006 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 1536) covalent geometry : angle 0.64969 ( 2085) hydrogen bonds : bond 0.02120 ( 14) hydrogen bonds : angle 5.44864 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.050 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0438 time to fit residues: 0.1824 Evaluate side-chains 2 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.129968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.108020 restraints weight = 1762.915| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.74 r_work: 0.3905 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1536 Z= 0.157 Angle : 0.498 4.993 2085 Z= 0.280 Chirality : 0.051 0.143 282 Planarity : 0.002 0.011 261 Dihedral : 5.260 19.789 228 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.72 % Allowed : 8.70 % Favored : 90.58 % 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: -2.17 (0.57), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.005 0.001 PHE A 94 HIS 0.007 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 1536) covalent geometry : angle 0.49804 ( 2085) hydrogen bonds : bond 0.01800 ( 14) hydrogen bonds : angle 5.42533 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.052 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 3 average time/residue: 0.0358 time to fit residues: 0.2087 Evaluate side-chains 3 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.130335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.108615 restraints weight = 1795.174| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.78 r_work: 0.3914 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1536 Z= 0.144 Angle : 0.475 4.795 2085 Z= 0.268 Chirality : 0.050 0.143 282 Planarity : 0.002 0.010 261 Dihedral : 4.984 18.369 228 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.72 % Allowed : 8.70 % Favored : 90.58 % 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: -2.13 (0.58), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.005 0.001 PHE C 94 HIS 0.007 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 1536) covalent geometry : angle 0.47482 ( 2085) hydrogen bonds : bond 0.01774 ( 14) hydrogen bonds : angle 5.38689 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.054 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0390 time to fit residues: 0.2660 Evaluate side-chains 4 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.132304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.110741 restraints weight = 1791.715| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.86 r_work: 0.3958 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1536 Z= 0.106 Angle : 0.420 3.916 2085 Z= 0.242 Chirality : 0.049 0.140 282 Planarity : 0.001 0.010 261 Dihedral : 4.650 17.881 228 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.72 % Allowed : 9.42 % Favored : 89.86 % 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: -2.07 (0.58), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 39 PHE 0.004 0.001 PHE A 94 HIS 0.006 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 1536) covalent geometry : angle 0.42015 ( 2085) hydrogen bonds : bond 0.01706 ( 14) hydrogen bonds : angle 5.38449 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.055 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0423 time to fit residues: 0.2906 Evaluate side-chains 4 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.128468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.106434 restraints weight = 1843.414| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.83 r_work: 0.3855 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1536 Z= 0.191 Angle : 0.526 5.630 2085 Z= 0.292 Chirality : 0.052 0.145 282 Planarity : 0.002 0.010 261 Dihedral : 5.186 18.324 228 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.72 % Allowed : 9.42 % Favored : 89.86 % 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: -2.15 (0.58), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.006 0.001 PHE A 94 HIS 0.008 0.005 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 1536) covalent geometry : angle 0.52620 ( 2085) hydrogen bonds : bond 0.01802 ( 14) hydrogen bonds : angle 5.27212 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.033 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0244 time to fit residues: 0.1662 Evaluate side-chains 4 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.126200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.103940 restraints weight = 1802.849| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.79 r_work: 0.3816 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 1536 Z= 0.240 Angle : 0.594 6.183 2085 Z= 0.328 Chirality : 0.054 0.161 282 Planarity : 0.002 0.011 261 Dihedral : 5.648 20.387 228 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.58), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 39 PHE 0.006 0.002 PHE A 94 HIS 0.009 0.005 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 1536) covalent geometry : angle 0.59415 ( 2085) hydrogen bonds : bond 0.01965 ( 14) hydrogen bonds : angle 5.34616 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 582.41 seconds wall clock time: 10 minutes 38.14 seconds (638.14 seconds total)