Starting phenix.real_space_refine on Fri Aug 22 12:39:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m6s_3451/08_2025/5m6s_3451.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m6s_3451/08_2025/5m6s_3451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5m6s_3451/08_2025/5m6s_3451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m6s_3451/08_2025/5m6s_3451.map" model { file = "/net/cci-nas-00/data/ceres_data/5m6s_3451/08_2025/5m6s_3451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m6s_3451/08_2025/5m6s_3451.cif" } resolution = 4.8 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 1 5.16 5 C 498 2.51 5 N 147 2.21 5 O 154 1.98 5 H 793 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1593 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1593 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Time building chain proxies: 0.99, per 1000 atoms: 0.62 Number of scatterers: 1593 At special positions: 0 Unit cell: (47.696, 70.46, 53.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 1 16.00 O 154 8.00 N 147 7.00 C 498 6.00 H 793 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 73.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 184 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 0 sheets defined 94.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 10 through 33 Processing helix chain 'A' and resid 37 through 77 removed outlier: 3.535A pdb=" N VAL A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 3.607A pdb=" N VAL A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 107 removed outlier: 3.945A pdb=" N ILE A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 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: 0.43 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 793 1.13 - 1.30: 146 1.30 - 1.46: 295 1.46 - 1.63: 369 1.63 - 1.80: 2 Bond restraints: 1605 Sorted by residual: bond pdb=" NZ LYS A 71 " pdb=" HZ2 LYS A 71 " ideal model delta sigma weight residual 0.890 1.042 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" CD1 TYR A 35 " pdb=" HD1 TYR A 35 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" NZ LYS A 47 " pdb=" HZ3 LYS A 47 " ideal model delta sigma weight residual 0.890 1.042 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CE1 HIS A 49 " pdb=" HE1 HIS A 49 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" CD2 HIS A 59 " pdb=" HD2 HIS A 59 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 1600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 2436 1.28 - 2.56: 244 2.56 - 3.83: 31 3.83 - 5.11: 91 5.11 - 6.39: 102 Bond angle restraints: 2904 Sorted by residual: angle pdb=" CA GLU A 60 " pdb=" C GLU A 60 " pdb=" N PRO A 61 " ideal model delta sigma weight residual 120.58 117.74 2.84 7.40e-01 1.83e+00 1.47e+01 angle pdb=" CD2 HIS A 49 " pdb=" NE2 HIS A 49 " pdb=" CE1 HIS A 49 " ideal model delta sigma weight residual 109.00 105.68 3.32 1.00e+00 1.00e+00 1.10e+01 angle pdb=" CD2 HIS A 10 " pdb=" NE2 HIS A 10 " pdb=" CE1 HIS A 10 " ideal model delta sigma weight residual 109.00 105.81 3.19 1.00e+00 1.00e+00 1.02e+01 angle pdb=" CD2 HIS A 94 " pdb=" NE2 HIS A 94 " pdb=" CE1 HIS A 94 " ideal model delta sigma weight residual 109.00 105.84 3.16 1.00e+00 1.00e+00 9.97e+00 angle pdb=" CD2 HIS A 59 " pdb=" NE2 HIS A 59 " pdb=" CE1 HIS A 59 " ideal model delta sigma weight residual 109.00 105.90 3.10 1.00e+00 1.00e+00 9.63e+00 ... (remaining 2899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 576 17.43 - 34.87: 64 34.87 - 52.30: 49 52.30 - 69.73: 35 69.73 - 87.16: 9 Dihedral angle restraints: 733 sinusoidal: 408 harmonic: 325 Sorted by residual: dihedral pdb=" CA ASP A 38 " pdb=" CB ASP A 38 " pdb=" CG ASP A 38 " pdb=" OD1 ASP A 38 " ideal model delta sinusoidal sigma weight residual -30.00 -86.45 56.45 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU A 55 " pdb=" CG GLU A 55 " pdb=" CD GLU A 55 " pdb=" OE1 GLU A 55 " ideal model delta sinusoidal sigma weight residual 0.00 -84.34 84.34 1 3.00e+01 1.11e-03 9.62e+00 dihedral pdb=" N SER A 21 " pdb=" CA SER A 21 " pdb=" CB SER A 21 " pdb=" OG SER A 21 " ideal model delta sinusoidal sigma weight residual 180.00 120.43 59.57 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 70 0.027 - 0.055: 28 0.055 - 0.082: 5 0.082 - 0.109: 6 0.109 - 0.136: 5 Chirality restraints: 114 Sorted by residual: chirality pdb=" CB THR A 78 " pdb=" CA THR A 78 " pdb=" OG1 THR A 78 " pdb=" CG2 THR A 78 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CB THR A 40 " pdb=" CA THR A 40 " pdb=" OG1 THR A 40 " pdb=" CG2 THR A 40 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 111 not shown) Planarity restraints: 239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 22 " 0.042 2.00e-02 2.50e+03 1.66e-02 1.10e+01 pdb=" CG TRP A 22 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP A 22 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 22 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 22 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 22 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 22 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 22 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 22 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 22 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 22 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP A 22 " -0.024 2.00e-02 2.50e+03 pdb=" HE3 TRP A 22 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 22 " 0.017 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 22 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP A 22 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 91 " 0.038 2.00e-02 2.50e+03 1.45e-02 6.29e+00 pdb=" CG PHE A 91 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 91 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 91 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 91 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 91 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 91 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 91 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE A 91 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 PHE A 91 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 91 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 91 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 59 " 0.022 2.00e-02 2.50e+03 1.63e-02 6.01e+00 pdb=" CG HIS A 59 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS A 59 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 59 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS A 59 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 59 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 HIS A 59 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 HIS A 59 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS A 59 " 0.031 2.00e-02 2.50e+03 ... (remaining 236 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 301 2.26 - 2.84: 3480 2.84 - 3.43: 4715 3.43 - 4.01: 5616 4.01 - 4.60: 8212 Nonbonded interactions: 22324 Sorted by model distance: nonbonded pdb=" H SER A 74 " pdb=" HG SER A 74 " model vdw 1.672 2.100 nonbonded pdb=" HG2 GLU A 20 " pdb="HH22 ARG A 87 " model vdw 1.711 2.270 nonbonded pdb=" HG3 GLU A 83 " pdb=" H ILE A 84 " model vdw 1.718 2.270 nonbonded pdb=" HG3 LYS A 47 " pdb=" HZ1 LYS A 47 " model vdw 1.737 2.270 nonbonded pdb=" HZ3 LYS A 26 " pdb=" HB3 GLU A 55 " model vdw 1.760 2.270 ... (remaining 22319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.020 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 6.160 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0401 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 0.019 812 Z= 0.356 Angle : 0.844 3.332 1086 Z= 0.685 Chirality : 0.044 0.136 114 Planarity : 0.003 0.013 143 Dihedral : 27.969 87.164 315 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 3.12 % Allowed : 7.29 % Favored : 89.58 % Rotamer: Outliers : 44.05 % Allowed : 16.67 % Favored : 39.29 % 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 aren not related in a simple way. whole: -5.37 (0.56), residues: 96 helix: -2.89 (0.37), residues: 86 sheet: None (None), residues: 0 loop : -7.05 (0.56), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 14 TYR 0.004 0.002 TYR A 35 PHE 0.022 0.004 PHE A 91 TRP 0.023 0.005 TRP A 22 HIS 0.003 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 812) covalent geometry : angle 0.84388 ( 1086) hydrogen bonds : bond 0.17810 ( 71) hydrogen bonds : angle 7.83883 ( 213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 15 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: -0.1857 (OUTLIER) cc_final: -0.4899 (m-30) REVERT: A 37 ARG cc_start: 0.4156 (OUTLIER) cc_final: 0.2532 (mmp-170) REVERT: A 50 LYS cc_start: -0.4981 (OUTLIER) cc_final: -0.5938 (mtpp) REVERT: A 75 ASP cc_start: 0.0709 (OUTLIER) cc_final: 0.0448 (m-30) outliers start: 37 outliers final: 16 residues processed: 45 average time/residue: 0.2260 time to fit residues: 10.5907 Evaluate side-chains 30 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 10 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.5271 r_free = 0.5271 target = 0.303901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5121 r_free = 0.5121 target = 0.262917 restraints weight = 6307.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.265280 restraints weight = 5205.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 14)----------------| | r_work = 0.5149 r_free = 0.5149 target = 0.267389 restraints weight = 4538.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.269685 restraints weight = 4097.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.5167 r_free = 0.5167 target = 0.271390 restraints weight = 3720.053| |-----------------------------------------------------------------------------| r_work (final): 0.5279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0163 moved from start: 0.7745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 812 Z= 0.207 Angle : 0.669 4.437 1086 Z= 0.373 Chirality : 0.034 0.129 114 Planarity : 0.005 0.034 143 Dihedral : 3.767 15.082 104 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.29 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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 aren not related in a simple way. whole: -0.10 (0.79), residues: 96 helix: 0.69 (0.50), residues: 87 sheet: None (None), residues: 0 loop : -7.28 (0.60), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 14 TYR 0.006 0.002 TYR A 35 PHE 0.006 0.002 PHE A 13 TRP 0.002 0.001 TRP A 22 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 812) covalent geometry : angle 0.66935 ( 1086) hydrogen bonds : bond 0.06099 ( 71) hydrogen bonds : angle 5.37314 ( 213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.2767 (mt) cc_final: 0.2518 (mp) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.2480 time to fit residues: 2.8839 Evaluate side-chains 7 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.5314 r_free = 0.5314 target = 0.321203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5178 r_free = 0.5178 target = 0.307886 restraints weight = 13264.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.311258 restraints weight = 9108.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.313764 restraints weight = 6496.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5263 r_free = 0.5263 target = 0.315450 restraints weight = 4696.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.316868 restraints weight = 3534.859| |-----------------------------------------------------------------------------| r_work (final): 0.5275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0624 moved from start: 0.9015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 812 Z= 0.145 Angle : 0.508 3.778 1086 Z= 0.289 Chirality : 0.030 0.121 114 Planarity : 0.004 0.020 143 Dihedral : 3.561 11.251 104 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.25 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 aren not related in a simple way. whole: 1.72 (0.88), residues: 96 helix: 1.96 (0.53), residues: 87 sheet: None (None), residues: 0 loop : -7.60 (0.58), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 87 TYR 0.004 0.002 TYR A 35 PHE 0.005 0.001 PHE A 13 TRP 0.009 0.001 TRP A 22 HIS 0.005 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 812) covalent geometry : angle 0.50770 ( 1086) hydrogen bonds : bond 0.05229 ( 71) hydrogen bonds : angle 4.60327 ( 213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: A 84 ILE cc_start: 0.1985 (mt) cc_final: 0.1770 (mp) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.2863 time to fit residues: 3.0233 Evaluate side-chains 8 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 60.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 7.2490 ------------------------------------------------------------------------------- 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 = 0.5217 r_free = 0.5217 target = 0.294580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.253061 restraints weight = 6876.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.254796 restraints weight = 6131.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.256434 restraints weight = 5521.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.257220 restraints weight = 5199.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.259184 restraints weight = 4968.001| |-----------------------------------------------------------------------------| r_work (final): 0.5098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0223 moved from start: 1.0321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 812 Z= 0.162 Angle : 0.556 3.761 1086 Z= 0.315 Chirality : 0.031 0.115 114 Planarity : 0.003 0.017 143 Dihedral : 3.966 15.592 104 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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 aren not related in a simple way. whole: 1.22 (0.83), residues: 96 helix: 1.61 (0.51), residues: 87 sheet: None (None), residues: 0 loop : -7.59 (0.59), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.004 0.002 TYR A 35 PHE 0.007 0.002 PHE A 12 TRP 0.009 0.001 TRP A 22 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 812) covalent geometry : angle 0.55554 ( 1086) hydrogen bonds : bond 0.05241 ( 71) hydrogen bonds : angle 4.57665 ( 213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.2235 (mt) cc_final: 0.1989 (mp) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.2981 time to fit residues: 2.8291 Evaluate side-chains 7 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 4.7490 ------------------------------------------------------------------------------- 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 = 0.5208 r_free = 0.5208 target = 0.290965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.253763 restraints weight = 6829.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.255690 restraints weight = 5909.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.258159 restraints weight = 5347.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.259960 restraints weight = 4909.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.261306 restraints weight = 4551.544| |-----------------------------------------------------------------------------| r_work (final): 0.5205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0037 moved from start: 1.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 812 Z= 0.123 Angle : 0.458 4.036 1086 Z= 0.260 Chirality : 0.028 0.115 114 Planarity : 0.003 0.016 143 Dihedral : 3.677 13.085 104 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.88), residues: 96 helix: 2.09 (0.53), residues: 87 sheet: None (None), residues: 0 loop : -7.47 (0.57), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.003 0.001 TYR A 35 PHE 0.008 0.002 PHE A 12 TRP 0.008 0.001 TRP A 22 HIS 0.005 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 812) covalent geometry : angle 0.45810 ( 1086) hydrogen bonds : bond 0.04648 ( 71) hydrogen bonds : angle 4.20337 ( 213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.2889 (mt) cc_final: 0.2506 (mt) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.2717 time to fit residues: 2.8686 Evaluate side-chains 8 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 3.7490 ------------------------------------------------------------------------------- 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 = 0.5215 r_free = 0.5215 target = 0.291895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.256415 restraints weight = 6759.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.259016 restraints weight = 5817.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.261327 restraints weight = 4953.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.263182 restraints weight = 4520.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.264258 restraints weight = 4227.756| |-----------------------------------------------------------------------------| r_work (final): 0.5178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0168 moved from start: 1.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 812 Z= 0.117 Angle : 0.474 3.927 1086 Z= 0.262 Chirality : 0.028 0.112 114 Planarity : 0.002 0.016 143 Dihedral : 3.806 14.636 104 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.89), residues: 96 helix: 2.29 (0.54), residues: 87 sheet: None (None), residues: 0 loop : -7.26 (0.61), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 51 TYR 0.003 0.001 TYR A 35 PHE 0.004 0.001 PHE A 13 TRP 0.008 0.001 TRP A 22 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 812) covalent geometry : angle 0.47410 ( 1086) hydrogen bonds : bond 0.04511 ( 71) hydrogen bonds : angle 4.10453 ( 213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.2099 (mt) cc_final: 0.1751 (mt) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.2730 time to fit residues: 2.5828 Evaluate side-chains 6 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 overall best weight: 5.7490 ------------------------------------------------------------------------------- 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 = 0.5237 r_free = 0.5237 target = 0.311319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.298550 restraints weight = 13317.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.301579 restraints weight = 9308.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5149 r_free = 0.5149 target = 0.304076 restraints weight = 6694.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5174 r_free = 0.5174 target = 0.306002 restraints weight = 4831.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5193 r_free = 0.5193 target = 0.307436 restraints weight = 3460.555| |-----------------------------------------------------------------------------| r_work (final): 0.5127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0335 moved from start: 1.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 812 Z= 0.138 Angle : 0.490 4.204 1086 Z= 0.277 Chirality : 0.029 0.106 114 Planarity : 0.003 0.015 143 Dihedral : 3.701 12.733 104 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.84), residues: 96 helix: 1.92 (0.52), residues: 87 sheet: None (None), residues: 0 loop : -6.53 (1.05), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 37 TYR 0.003 0.001 TYR A 35 PHE 0.007 0.001 PHE A 13 TRP 0.008 0.001 TRP A 22 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 812) covalent geometry : angle 0.48971 ( 1086) hydrogen bonds : bond 0.04648 ( 71) hydrogen bonds : angle 4.22042 ( 213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.2350 (mt) cc_final: 0.2068 (mt) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.2833 time to fit residues: 2.6795 Evaluate side-chains 5 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 6.7490 ------------------------------------------------------------------------------- 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 = 0.5198 r_free = 0.5198 target = 0.308327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.296034 restraints weight = 13367.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.298989 restraints weight = 9340.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.301497 restraints weight = 6804.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.303129 restraints weight = 4809.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.304499 restraints weight = 3521.075| |-----------------------------------------------------------------------------| r_work (final): 0.5154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0738 moved from start: 1.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 812 Z= 0.137 Angle : 0.513 4.790 1086 Z= 0.283 Chirality : 0.028 0.107 114 Planarity : 0.003 0.015 143 Dihedral : 3.985 16.223 104 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.86), residues: 96 helix: 1.97 (0.53), residues: 87 sheet: None (None), residues: 0 loop : -6.37 (1.18), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.008 0.002 TYR A 35 PHE 0.009 0.002 PHE A 13 TRP 0.009 0.002 TRP A 22 HIS 0.003 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 812) covalent geometry : angle 0.51278 ( 1086) hydrogen bonds : bond 0.04717 ( 71) hydrogen bonds : angle 4.09587 ( 213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.1780 (mt) cc_final: 0.1545 (mt) REVERT: A 87 ARG cc_start: 0.6908 (tmt-80) cc_final: 0.5709 (mmp80) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.3897 time to fit residues: 3.6463 Evaluate side-chains 7 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 overall best weight: 5.2490 ------------------------------------------------------------------------------- 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 = 0.5213 r_free = 0.5213 target = 0.308842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.295857 restraints weight = 13399.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.298994 restraints weight = 9312.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.301484 restraints weight = 6688.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.303558 restraints weight = 4888.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5164 r_free = 0.5164 target = 0.304935 restraints weight = 3352.730| |-----------------------------------------------------------------------------| r_work (final): 0.5084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0414 moved from start: 1.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 812 Z= 0.126 Angle : 0.494 4.347 1086 Z= 0.271 Chirality : 0.028 0.104 114 Planarity : 0.002 0.014 143 Dihedral : 3.867 13.122 104 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.88), residues: 96 helix: 2.03 (0.54), residues: 87 sheet: None (None), residues: 0 loop : -6.30 (1.23), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 37 TYR 0.001 0.000 TYR A 35 PHE 0.006 0.001 PHE A 13 TRP 0.008 0.001 TRP A 22 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 812) covalent geometry : angle 0.49376 ( 1086) hydrogen bonds : bond 0.04482 ( 71) hydrogen bonds : angle 4.02633 ( 213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: A 84 ILE cc_start: 0.2352 (mt) cc_final: 0.1921 (mt) REVERT: A 87 ARG cc_start: 0.7334 (tmt-80) cc_final: 0.6552 (mmp80) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.3845 time to fit residues: 3.5822 Evaluate side-chains 7 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 5.2490 ------------------------------------------------------------------------------- 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 = 0.5199 r_free = 0.5199 target = 0.307181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.294418 restraints weight = 13644.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.297598 restraints weight = 9314.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.300045 restraints weight = 6624.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.301984 restraints weight = 4756.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.303218 restraints weight = 3291.972| |-----------------------------------------------------------------------------| r_work (final): 0.5150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0660 moved from start: 1.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 812 Z= 0.130 Angle : 0.521 4.918 1086 Z= 0.283 Chirality : 0.029 0.106 114 Planarity : 0.004 0.025 143 Dihedral : 4.131 18.305 104 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.86), residues: 96 helix: 1.86 (0.53), residues: 87 sheet: None (None), residues: 0 loop : -6.03 (1.51), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.013 0.003 TYR A 35 PHE 0.006 0.002 PHE A 13 TRP 0.010 0.002 TRP A 22 HIS 0.003 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 812) covalent geometry : angle 0.52137 ( 1086) hydrogen bonds : bond 0.04600 ( 71) hydrogen bonds : angle 3.90027 ( 213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.3491 time to fit residues: 3.2690 Evaluate side-chains 7 residues out of total 84 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 overall best weight: 5.4990 ------------------------------------------------------------------------------- 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 = 0.5184 r_free = 0.5184 target = 0.307397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.295012 restraints weight = 13323.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.298467 restraints weight = 9050.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.300923 restraints weight = 6255.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.302567 restraints weight = 4314.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.303650 restraints weight = 3012.302| |-----------------------------------------------------------------------------| r_work (final): 0.5139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0628 moved from start: 1.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 812 Z= 0.123 Angle : 0.506 4.693 1086 Z= 0.278 Chirality : 0.028 0.105 114 Planarity : 0.002 0.013 143 Dihedral : 3.946 11.770 104 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.89), residues: 96 helix: 1.86 (0.55), residues: 87 sheet: None (None), residues: 0 loop : -6.04 (1.47), residues: 9 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 37 TYR 0.001 0.001 TYR A 35 PHE 0.006 0.001 PHE A 13 TRP 0.009 0.002 TRP A 22 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 812) covalent geometry : angle 0.50583 ( 1086) hydrogen bonds : bond 0.04454 ( 71) hydrogen bonds : angle 3.84172 ( 213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 627.05 seconds wall clock time: 11 minutes 53.29 seconds (713.29 seconds total)