Starting phenix.real_space_refine on Tue Feb 3 11:21:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y31_72430/02_2026/9y31_72430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y31_72430/02_2026/9y31_72430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y31_72430/02_2026/9y31_72430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y31_72430/02_2026/9y31_72430.map" model { file = "/net/cci-nas-00/data/ceres_data/9y31_72430/02_2026/9y31_72430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y31_72430/02_2026/9y31_72430.cif" } resolution = 3.62 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= -0.005 sd= 0.177 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 274 2.51 5 N 79 2.21 5 O 80 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 433 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} Chain: "E" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 136 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 144 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Time building chain proxies: 0.14, per 1000 atoms: 0.32 Number of scatterers: 433 At special positions: 0 Unit cell: (65.9928, 65.9928, 64.9284, 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 80 8.00 N 79 7.00 C 274 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.04 Conformation dependent library (CDL) restraints added in 11.5 milliseconds 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 114 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.01 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 57 through 59 2 hydrogen bonds defined for protein. 6 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: 0.02 Time building geometry restraints manager: 0.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 65 1.28 - 1.35: 90 1.35 - 1.43: 18 1.43 - 1.50: 135 1.50 - 1.57: 131 Bond restraints: 439 Sorted by residual: bond pdb=" CB VAL C 62 " pdb=" CG2 VAL C 62 " ideal model delta sigma weight residual 1.521 1.406 0.115 3.30e-02 9.18e+02 1.22e+01 bond pdb=" CB VAL H 62 " pdb=" CG2 VAL H 62 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.11e+01 bond pdb=" CA ALA E 65 " pdb=" CB ALA E 65 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.51e-02 4.39e+03 9.84e+00 bond pdb=" CA TYR E 66 " pdb=" CB TYR E 66 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.48e-02 4.57e+03 9.55e+00 bond pdb=" CB VAL E 62 " pdb=" CG2 VAL E 62 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.51e+00 ... (remaining 434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 450 1.97 - 3.93: 113 3.93 - 5.89: 29 5.89 - 7.85: 5 7.85 - 9.81: 2 Bond angle restraints: 599 Sorted by residual: angle pdb=" C LEU C 58 " pdb=" N SER C 59 " pdb=" CA SER C 59 " ideal model delta sigma weight residual 121.54 131.35 -9.81 1.91e+00 2.74e-01 2.64e+01 angle pdb=" C ARG E 67 " pdb=" N GLU E 68 " pdb=" CA GLU E 68 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N ARG C 57 " pdb=" CA ARG C 57 " pdb=" C ARG C 57 " ideal model delta sigma weight residual 109.76 103.75 6.01 1.59e+00 3.96e-01 1.43e+01 angle pdb=" N ALA C 65 " pdb=" CA ALA C 65 " pdb=" C ALA C 65 " ideal model delta sigma weight residual 107.20 113.30 -6.10 1.70e+00 3.46e-01 1.29e+01 angle pdb=" N LEU H 58 " pdb=" CA LEU H 58 " pdb=" C LEU H 58 " ideal model delta sigma weight residual 113.18 117.58 -4.40 1.33e+00 5.65e-01 1.10e+01 ... (remaining 594 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 13.86: 240 13.86 - 27.69: 29 27.69 - 41.53: 9 41.53 - 55.37: 0 55.37 - 69.21: 1 Dihedral angle restraints: 279 sinusoidal: 108 harmonic: 171 Sorted by residual: dihedral pdb=" CA GLU E 68 " pdb=" C GLU E 68 " pdb=" N VAL E 69 " pdb=" CA VAL E 69 " ideal model delta harmonic sigma weight residual -180.00 -146.74 -33.26 0 5.00e+00 4.00e-02 4.42e+01 dihedral pdb=" CA ARG E 67 " pdb=" C ARG E 67 " pdb=" N GLU E 68 " pdb=" CA GLU E 68 " ideal model delta harmonic sigma weight residual 180.00 149.90 30.10 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA THR E 71 " pdb=" C THR E 71 " pdb=" N GLN E 72 " pdb=" CA GLN E 72 " ideal model delta harmonic sigma weight residual 180.00 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 52 0.083 - 0.165: 16 0.165 - 0.248: 7 0.248 - 0.330: 1 0.330 - 0.413: 1 Chirality restraints: 77 Sorted by residual: chirality pdb=" CG LEU E 58 " pdb=" CB LEU E 58 " pdb=" CD1 LEU E 58 " pdb=" CD2 LEU E 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA GLU E 68 " pdb=" N GLU E 68 " pdb=" C GLU E 68 " pdb=" CB GLU E 68 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA PRO H 73 " pdb=" N PRO H 73 " pdb=" C PRO H 73 " pdb=" CB PRO H 73 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 74 not shown) Planarity restraints: 74 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 72 " 0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO C 73 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO C 73 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 73 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 67 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ARG E 67 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG E 67 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU E 68 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 60 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C ALA H 60 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA H 60 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO H 61 " -0.011 2.00e-02 2.50e+03 ... (remaining 71 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 222 3.03 - 3.49: 360 3.49 - 3.96: 476 3.96 - 4.43: 494 4.43 - 4.90: 794 Nonbonded interactions: 2346 Sorted by model distance: nonbonded pdb=" CB LYS C 54 " pdb=" N VAL C 55 " model vdw 2.557 2.816 nonbonded pdb=" N LEU C 64 " pdb=" O LEU C 64 " model vdw 2.588 2.496 nonbonded pdb=" C SER C 59 " pdb=" OG SER C 59 " model vdw 2.594 2.616 nonbonded pdb=" N ALA H 63 " pdb=" O ALA H 63 " model vdw 2.596 2.496 nonbonded pdb=" N TYR E 66 " pdb=" O TYR E 66 " model vdw 2.598 2.496 ... (remaining 2341 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 56 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1)) or resid 69 through 7 \ 3)) selection = chain 'E' selection = (chain 'H' and (resid 56 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1)) or resid 69 through 7 \ 3)) } 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: 10.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 1.720 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.031 0.341 440 Z= 1.956 Angle : 1.912 9.813 599 Z= 1.029 Chirality : 0.104 0.413 77 Planarity : 0.018 0.094 74 Dihedral : 13.940 69.206 165 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 1.96 % Allowed : 23.53 % Favored : 74.51 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.17 % 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: -6.03 (0.74), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.57), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG C 67 TYR 0.016 0.004 TYR C 66 Details of bonding type rmsd covalent geometry : bond 0.02634 ( 439) covalent geometry : angle 1.91228 ( 599) hydrogen bonds : bond 0.37245 ( 2) hydrogen bonds : angle 8.30313 ( 6) Misc. bond : bond 0.34080 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.010 Fit side-chains REVERT: C 67 ARG cc_start: 0.7439 (pmt-80) cc_final: 0.6362 (mmt180) REVERT: C 72 GLN cc_start: 0.8138 (pm20) cc_final: 0.7811 (mm-40) REVERT: E 57 ARG cc_start: 0.8887 (mtm180) cc_final: 0.8647 (mtp180) REVERT: H 59 SER cc_start: 0.8851 (t) cc_final: 0.8616 (p) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0693 time to fit residues: 1.0742 Evaluate side-chains 12 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 overall best weight: 3.4990 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.129020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107892 restraints weight = 1176.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108399 restraints weight = 1034.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108857 restraints weight = 973.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108913 restraints weight = 932.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108927 restraints weight = 923.275| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 440 Z= 0.168 Angle : 0.709 6.916 599 Z= 0.369 Chirality : 0.041 0.112 77 Planarity : 0.006 0.041 74 Dihedral : 6.034 16.824 63 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Rotamer: Outliers : 0.00 % Allowed : 22.92 % Favored : 77.08 % 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: -5.65 (0.82), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.63), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 67 TYR 0.005 0.001 TYR H 66 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 439) covalent geometry : angle 0.70876 ( 599) hydrogen bonds : bond 0.02975 ( 2) hydrogen bonds : angle 5.36499 ( 6) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7356 (pmt-80) cc_final: 0.5799 (mmt180) REVERT: C 72 GLN cc_start: 0.8143 (pm20) cc_final: 0.7531 (mm-40) REVERT: E 57 ARG cc_start: 0.8583 (mtm180) cc_final: 0.8236 (mtp180) REVERT: H 59 SER cc_start: 0.8727 (t) cc_final: 0.8385 (p) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0678 time to fit residues: 1.0519 Evaluate side-chains 14 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 4.4990 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.128541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.107233 restraints weight = 1100.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107781 restraints weight = 981.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108036 restraints weight = 924.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108339 restraints weight = 898.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108339 restraints weight = 875.575| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 440 Z= 0.188 Angle : 0.705 7.114 599 Z= 0.369 Chirality : 0.041 0.112 77 Planarity : 0.006 0.038 74 Dihedral : 5.114 15.194 63 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 1.96 % Allowed : 21.57 % Favored : 76.47 % Rotamer: Outliers : 2.08 % Allowed : 25.00 % Favored : 72.92 % 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: -5.64 (0.83), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.63), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 57 TYR 0.005 0.001 TYR H 66 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 439) covalent geometry : angle 0.70531 ( 599) hydrogen bonds : bond 0.03295 ( 2) hydrogen bonds : angle 5.03864 ( 6) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7099 (pmt-80) cc_final: 0.5768 (mmt180) REVERT: C 72 GLN cc_start: 0.8096 (pm20) cc_final: 0.7532 (mm-40) REVERT: E 57 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8166 (mtp180) REVERT: H 57 ARG cc_start: 0.8422 (mpp80) cc_final: 0.8125 (mpp80) REVERT: H 59 SER cc_start: 0.8782 (t) cc_final: 0.8420 (p) outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.0775 time to fit residues: 1.1978 Evaluate side-chains 15 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 overall best weight: 6.4990 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.126947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106977 restraints weight = 1139.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106998 restraints weight = 1085.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106998 restraints weight = 1082.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106998 restraints weight = 1082.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106998 restraints weight = 1082.224| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 440 Z= 0.248 Angle : 0.784 6.771 599 Z= 0.407 Chirality : 0.043 0.124 77 Planarity : 0.007 0.040 74 Dihedral : 5.427 14.420 63 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 1.96 % Allowed : 19.61 % Favored : 78.43 % Rotamer: Outliers : 6.25 % Allowed : 29.17 % Favored : 64.58 % 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: -5.58 (0.82), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.63), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 67 TYR 0.006 0.001 TYR H 66 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 439) covalent geometry : angle 0.78422 ( 599) hydrogen bonds : bond 0.03952 ( 2) hydrogen bonds : angle 5.08515 ( 6) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7245 (pmt-80) cc_final: 0.5755 (mmt180) REVERT: C 72 GLN cc_start: 0.8110 (pm20) cc_final: 0.7446 (mm-40) REVERT: E 57 ARG cc_start: 0.8630 (mtm180) cc_final: 0.8316 (mtp180) REVERT: E 58 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8376 (mm) REVERT: H 59 SER cc_start: 0.8834 (t) cc_final: 0.8490 (p) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.0599 time to fit residues: 1.0549 Evaluate side-chains 17 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 3 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 = 0.3676 r_free = 0.3676 target = 0.127252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106951 restraints weight = 1155.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106951 restraints weight = 1093.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106951 restraints weight = 1093.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106951 restraints weight = 1093.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106951 restraints weight = 1093.046| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.029 440 Z= 0.263 Angle : 0.803 6.503 599 Z= 0.416 Chirality : 0.043 0.120 77 Planarity : 0.007 0.039 74 Dihedral : 5.425 14.480 63 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 1.96 % Allowed : 23.53 % Favored : 74.51 % Rotamer: Outliers : 8.33 % Allowed : 25.00 % Favored : 66.67 % 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: -5.65 (0.80), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.61), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 67 TYR 0.006 0.001 TYR H 66 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 439) covalent geometry : angle 0.80299 ( 599) hydrogen bonds : bond 0.03901 ( 2) hydrogen bonds : angle 5.03228 ( 6) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7053 (pmt-80) cc_final: 0.5676 (mmt180) REVERT: C 72 GLN cc_start: 0.8075 (pm20) cc_final: 0.7459 (mm-40) REVERT: E 57 ARG cc_start: 0.8574 (mtm180) cc_final: 0.8309 (mtp180) REVERT: E 58 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8412 (mm) REVERT: H 59 SER cc_start: 0.8837 (t) cc_final: 0.8482 (p) outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.0569 time to fit residues: 1.0614 Evaluate side-chains 18 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.0070 overall best weight: 3.5030 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.129147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107701 restraints weight = 1156.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107709 restraints weight = 1032.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107709 restraints weight = 1031.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107709 restraints weight = 1031.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107709 restraints weight = 1031.412| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 440 Z= 0.155 Angle : 0.671 6.724 599 Z= 0.354 Chirality : 0.039 0.111 77 Planarity : 0.005 0.032 74 Dihedral : 4.707 14.682 63 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % Rotamer: Outliers : 8.33 % Allowed : 27.08 % Favored : 64.58 % 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: -5.60 (0.79), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.26 (0.61), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 67 TYR 0.005 0.001 TYR H 66 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 439) covalent geometry : angle 0.67104 ( 599) hydrogen bonds : bond 0.02976 ( 2) hydrogen bonds : angle 5.09268 ( 6) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7036 (pmt-80) cc_final: 0.5584 (mmt180) REVERT: C 72 GLN cc_start: 0.8070 (pm20) cc_final: 0.7396 (mm-40) REVERT: E 57 ARG cc_start: 0.8575 (mtm180) cc_final: 0.8242 (mtp180) REVERT: E 58 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8422 (mm) REVERT: H 59 SER cc_start: 0.8771 (t) cc_final: 0.8420 (p) outliers start: 4 outliers final: 3 residues processed: 17 average time/residue: 0.0588 time to fit residues: 1.0366 Evaluate side-chains 17 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 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 = 0.3674 r_free = 0.3674 target = 0.126885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105847 restraints weight = 1116.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106333 restraints weight = 1011.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106334 restraints weight = 961.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106334 restraints weight = 961.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106334 restraints weight = 961.548| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 440 Z= 0.262 Angle : 0.800 6.230 599 Z= 0.414 Chirality : 0.043 0.118 77 Planarity : 0.007 0.037 74 Dihedral : 5.208 13.532 63 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 1.96 % Allowed : 23.53 % Favored : 74.51 % Rotamer: Outliers : 8.33 % Allowed : 27.08 % Favored : 64.58 % 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: -5.70 (0.79), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.60), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 67 TYR 0.005 0.001 TYR H 66 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 439) covalent geometry : angle 0.79963 ( 599) hydrogen bonds : bond 0.03914 ( 2) hydrogen bonds : angle 4.89459 ( 6) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.010 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7086 (pmt-80) cc_final: 0.5685 (mmt180) REVERT: C 72 GLN cc_start: 0.8097 (pm20) cc_final: 0.7457 (mm-40) REVERT: E 57 ARG cc_start: 0.8637 (mtm180) cc_final: 0.8363 (mtp180) REVERT: E 58 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8401 (mm) REVERT: H 59 SER cc_start: 0.8887 (t) cc_final: 0.8571 (p) outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.0554 time to fit residues: 1.0352 Evaluate side-chains 18 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 0.0870 overall best weight: 4.0430 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.129046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108216 restraints weight = 1169.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108574 restraints weight = 1097.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108574 restraints weight = 1056.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108574 restraints weight = 1056.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108574 restraints weight = 1056.943| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 440 Z= 0.173 Angle : 0.701 6.479 599 Z= 0.369 Chirality : 0.040 0.114 77 Planarity : 0.006 0.032 74 Dihedral : 4.721 14.053 63 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % Rotamer: Outliers : 10.42 % Allowed : 29.17 % Favored : 60.42 % 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: -5.64 (0.80), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.61), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 57 TYR 0.005 0.001 TYR C 66 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 439) covalent geometry : angle 0.70144 ( 599) hydrogen bonds : bond 0.03121 ( 2) hydrogen bonds : angle 4.92567 ( 6) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7075 (pmt-80) cc_final: 0.5593 (mmt180) REVERT: C 72 GLN cc_start: 0.8039 (pm20) cc_final: 0.7331 (mm-40) REVERT: E 57 ARG cc_start: 0.8598 (mtm180) cc_final: 0.8275 (mtp180) REVERT: E 58 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8426 (mm) REVERT: H 59 SER cc_start: 0.8746 (t) cc_final: 0.8382 (p) outliers start: 5 outliers final: 4 residues processed: 17 average time/residue: 0.0601 time to fit residues: 1.0601 Evaluate side-chains 18 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 overall best weight: 6.4990 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.127746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106888 restraints weight = 1204.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107151 restraints weight = 1132.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107151 restraints weight = 1096.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107151 restraints weight = 1096.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107151 restraints weight = 1096.953| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 440 Z= 0.250 Angle : 0.790 6.125 599 Z= 0.411 Chirality : 0.043 0.118 77 Planarity : 0.007 0.035 74 Dihedral : 5.060 13.448 63 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 1.96 % Allowed : 23.53 % Favored : 74.51 % Rotamer: Outliers : 12.50 % Allowed : 27.08 % Favored : 60.42 % 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: -5.71 (0.79), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.61), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 67 TYR 0.005 0.001 TYR H 66 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 439) covalent geometry : angle 0.78967 ( 599) hydrogen bonds : bond 0.03845 ( 2) hydrogen bonds : angle 4.88454 ( 6) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7180 (pmt-80) cc_final: 0.5716 (mmt180) REVERT: C 72 GLN cc_start: 0.8107 (pm20) cc_final: 0.7418 (mm-40) REVERT: E 57 ARG cc_start: 0.8653 (mtm180) cc_final: 0.8370 (mtp180) REVERT: E 58 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8414 (mm) REVERT: H 59 SER cc_start: 0.8881 (t) cc_final: 0.8567 (p) outliers start: 6 outliers final: 5 residues processed: 17 average time/residue: 0.0603 time to fit residues: 1.0629 Evaluate side-chains 19 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 3 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 = 0.3720 r_free = 0.3720 target = 0.130046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109196 restraints weight = 1161.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109271 restraints weight = 1109.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109408 restraints weight = 1097.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109408 restraints weight = 1077.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109408 restraints weight = 1077.378| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 440 Z= 0.170 Angle : 0.706 6.545 599 Z= 0.372 Chirality : 0.039 0.112 77 Planarity : 0.006 0.032 74 Dihedral : 4.609 14.146 63 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % Rotamer: Outliers : 12.50 % Allowed : 27.08 % Favored : 60.42 % 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: -5.62 (0.80), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.61), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 67 TYR 0.005 0.001 TYR C 66 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 439) covalent geometry : angle 0.70637 ( 599) hydrogen bonds : bond 0.03052 ( 2) hydrogen bonds : angle 4.88180 ( 6) Misc. bond : bond 0.00024 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 102 Ramachandran restraints generated. 51 Oldfield, 0 Emsley, 51 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7069 (pmt-80) cc_final: 0.5589 (mmt180) REVERT: C 72 GLN cc_start: 0.8022 (pm20) cc_final: 0.7329 (mm-40) REVERT: E 57 ARG cc_start: 0.8588 (mtm180) cc_final: 0.8265 (mtp180) REVERT: E 58 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8440 (mm) REVERT: H 59 SER cc_start: 0.8782 (t) cc_final: 0.8438 (p) outliers start: 6 outliers final: 5 residues processed: 15 average time/residue: 0.0682 time to fit residues: 1.0571 Evaluate side-chains 17 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 10.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.128483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107786 restraints weight = 1154.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107984 restraints weight = 1106.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107984 restraints weight = 1086.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107984 restraints weight = 1086.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107984 restraints weight = 1086.094| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 440 Z= 0.231 Angle : 0.770 6.188 599 Z= 0.401 Chirality : 0.042 0.115 77 Planarity : 0.006 0.034 74 Dihedral : 4.879 13.527 63 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 1.96 % Allowed : 23.53 % Favored : 74.51 % Rotamer: Outliers : 12.50 % Allowed : 27.08 % Favored : 60.42 % 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: -5.68 (0.80), residues: 51 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.61), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 67 TYR 0.005 0.001 TYR C 66 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 439) covalent geometry : angle 0.77042 ( 599) hydrogen bonds : bond 0.03683 ( 2) hydrogen bonds : angle 4.82843 ( 6) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 362.64 seconds wall clock time: 6 minutes 38.34 seconds (398.34 seconds total)