Starting phenix.real_space_refine on Tue Aug 4 11:45:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9t_65788/08_2026/9w9t_65788.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9t_65788/08_2026/9w9t_65788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9t_65788/08_2026/9w9t_65788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9t_65788/08_2026/9w9t_65788.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9t_65788/08_2026/9w9t_65788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9t_65788/08_2026/9w9t_65788.cif" } resolution = 2.83 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 1239 2.51 5 N 321 2.21 5 O 342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1905 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 635 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 0.73, per 1000 atoms: 0.38 Number of scatterers: 1905 At special positions: 0 Unit cell: (66.96, 86.49, 30.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 342 8.00 N 321 7.00 C 1239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 70.7 milliseconds 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 468 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 45.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 16 removed outlier: 6.418A pdb=" N VAL A 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.410A pdb=" N ALA A 19 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.610A pdb=" N ILE A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.342A pdb=" N HIS A 31 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 70 through 73 removed outlier: 6.438A pdb=" N LYS A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE C 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU A 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.929A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N LYS A 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N TRP C 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 97 removed outlier: 6.311A pdb=" N GLU A 89 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLU B 92 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA A 91 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL B 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 93 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR B 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE A 95 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N HIS A 90 " --> pdb=" O GLU C 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 110 removed outlier: 6.947A pdb=" N ALA A 109 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B 110 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG A 104 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE C 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 106 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA C 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA A 108 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.920A pdb=" N TYR A 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 118 through 122 removed outlier: 5.695A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) 32 hydrogen bonds defined for protein. 96 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: 0.28 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 582 1.34 - 1.46: 322 1.46 - 1.57: 1043 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 1953 Sorted by residual: bond pdb=" CA PHE A 33 " pdb=" C PHE A 33 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.12e-02 7.97e+03 8.20e-01 bond pdb=" CA PHE B 33 " pdb=" C PHE B 33 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.12e-02 7.97e+03 8.09e-01 bond pdb=" CA PHE C 33 " pdb=" C PHE C 33 " ideal model delta sigma weight residual 1.520 1.529 -0.010 1.12e-02 7.97e+03 7.31e-01 bond pdb=" CA VAL B 94 " pdb=" CB VAL B 94 " ideal model delta sigma weight residual 1.531 1.540 -0.009 1.11e-02 8.12e+03 6.60e-01 bond pdb=" CA SER A 100 " pdb=" C SER A 100 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.08e-02 8.57e+03 6.12e-01 ... (remaining 1948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 2441 1.01 - 2.02: 159 2.02 - 3.03: 41 3.03 - 4.03: 11 4.03 - 5.04: 6 Bond angle restraints: 2658 Sorted by residual: angle pdb=" N SER C 100 " pdb=" CA SER C 100 " pdb=" C SER C 100 " ideal model delta sigma weight residual 107.32 112.14 -4.82 1.65e+00 3.67e-01 8.53e+00 angle pdb=" N SER B 100 " pdb=" CA SER B 100 " pdb=" C SER B 100 " ideal model delta sigma weight residual 107.32 112.13 -4.81 1.65e+00 3.67e-01 8.52e+00 angle pdb=" N SER A 100 " pdb=" CA SER A 100 " pdb=" C SER A 100 " ideal model delta sigma weight residual 107.32 112.12 -4.80 1.65e+00 3.67e-01 8.46e+00 angle pdb=" C ILE A 84 " pdb=" N SER A 85 " pdb=" CA SER A 85 " ideal model delta sigma weight residual 123.15 120.32 2.83 1.21e+00 6.83e-01 5.45e+00 angle pdb=" C ILE C 84 " pdb=" N SER C 85 " pdb=" CA SER C 85 " ideal model delta sigma weight residual 123.15 120.33 2.82 1.21e+00 6.83e-01 5.43e+00 ... (remaining 2653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.85: 992 10.85 - 21.71: 112 21.71 - 32.56: 36 32.56 - 43.41: 9 43.41 - 54.27: 9 Dihedral angle restraints: 1158 sinusoidal: 438 harmonic: 720 Sorted by residual: dihedral pdb=" CA ILE C 26 " pdb=" C ILE C 26 " pdb=" N ASN C 27 " pdb=" CA ASN C 27 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 dihedral pdb=" CA ILE A 26 " pdb=" C ILE A 26 " pdb=" N ASN A 27 " pdb=" CA ASN A 27 " ideal model delta harmonic sigma weight residual 180.00 164.60 15.40 0 5.00e+00 4.00e-02 9.49e+00 dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N ASN B 27 " pdb=" CA ASN B 27 " ideal model delta harmonic sigma weight residual 180.00 164.64 15.36 0 5.00e+00 4.00e-02 9.44e+00 ... (remaining 1155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 167 0.024 - 0.048: 60 0.048 - 0.071: 41 0.071 - 0.095: 31 0.095 - 0.119: 16 Chirality restraints: 315 Sorted by residual: chirality pdb=" CA VAL C 121 " pdb=" N VAL C 121 " pdb=" C VAL C 121 " pdb=" CB VAL C 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA VAL A 121 " pdb=" N VAL A 121 " pdb=" C VAL A 121 " pdb=" CB VAL A 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA VAL B 121 " pdb=" N VAL B 121 " pdb=" C VAL B 121 " pdb=" CB VAL B 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 312 not shown) Planarity restraints: 321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 114 " -0.009 2.00e-02 2.50e+03 7.10e-03 1.01e+00 pdb=" CG TYR B 114 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 114 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 114 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 114 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 100 " 0.005 2.00e-02 2.50e+03 9.88e-03 9.75e-01 pdb=" C SER C 100 " -0.017 2.00e-02 2.50e+03 pdb=" O SER C 100 " 0.006 2.00e-02 2.50e+03 pdb=" N GLY C 101 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 100 " 0.005 2.00e-02 2.50e+03 9.84e-03 9.68e-01 pdb=" C SER A 100 " -0.017 2.00e-02 2.50e+03 pdb=" O SER A 100 " 0.006 2.00e-02 2.50e+03 pdb=" N GLY A 101 " 0.006 2.00e-02 2.50e+03 ... (remaining 318 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 471 2.82 - 3.34: 1538 3.34 - 3.86: 3168 3.86 - 4.38: 3493 4.38 - 4.90: 6474 Nonbonded interactions: 15144 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OH TYR B 105 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR A 105 " pdb=" OD2 ASP C 74 " model vdw 2.300 3.040 nonbonded pdb=" NZ LYS A 76 " pdb=" OD1 ASP B 74 " model vdw 2.302 3.120 nonbonded pdb=" OD1 ASP A 74 " pdb=" NZ LYS C 76 " model vdw 2.308 3.120 nonbonded pdb=" OD1 ASP C 99 " pdb=" NH1 ARG C 103 " model vdw 2.425 3.120 ... (remaining 15139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.870 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.002 0.025 1953 Z= 0.142 Angle : 0.651 5.043 2658 Z= 0.390 Chirality : 0.045 0.119 315 Planarity : 0.005 0.032 321 Dihedral : 12.331 54.266 690 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.48), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 104 TYR 0.017 0.001 TYR B 114 PHE 0.002 0.000 PHE A 95 TRP 0.005 0.001 TRP A 79 HIS 0.001 0.000 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 ( 1953) covalent geometry : angle 0.65056 / 0.39 ( 2658) hydrogen bonds : bond 0.16216 / 9.38 ( 32) hydrogen bonds : angle 9.36770 / 6.61 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7796 (mt-10) REVERT: A 74 ASP cc_start: 0.8371 (t0) cc_final: 0.8066 (t70) REVERT: B 13 MET cc_start: 0.6899 (ttm) cc_final: 0.6279 (tmm) REVERT: B 72 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7840 (mt-10) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.8266 time to fit residues: 26.0196 Evaluate side-chains 29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099030 restraints weight = 2328.402| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.81 r_work: 0.3255 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 1953 Z= 0.262 Angle : 0.670 4.249 2658 Z= 0.371 Chirality : 0.051 0.131 315 Planarity : 0.005 0.026 321 Dihedral : 5.262 21.417 264 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.90 % Allowed : 22.38 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.50), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.022 0.002 TYR A 114 PHE 0.011 0.002 PHE A 87 TRP 0.006 0.002 TRP B 79 HIS 0.007 0.002 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.26 ( 1953) covalent geometry : angle 0.67046 / 0.37 ( 2658) hydrogen bonds : bond 0.04062 / 2.45 ( 32) hydrogen bonds : angle 6.06863 / 4.22 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7164 (mt) REVERT: C 13 MET cc_start: 0.6597 (ttm) cc_final: 0.6262 (tpt) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 0.7206 time to fit residues: 26.3649 Evaluate side-chains 33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103294 restraints weight = 2264.297| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.82 r_work: 0.3331 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1953 Z= 0.127 Angle : 0.521 4.234 2658 Z= 0.285 Chirality : 0.048 0.132 315 Planarity : 0.003 0.018 321 Dihedral : 4.895 19.795 264 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.43 % Allowed : 23.33 % Favored : 75.24 % 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 are not related in a simple way. whole: -2.61 (0.52), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.019 0.002 TYR A 114 PHE 0.005 0.001 PHE C 87 TRP 0.004 0.001 TRP C 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 1953) covalent geometry : angle 0.52121 / 0.28 ( 2658) hydrogen bonds : bond 0.02708 / 1.78 ( 32) hydrogen bonds : angle 5.31357 / 3.78 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7088 (mt) REVERT: C 13 MET cc_start: 0.6652 (ttm) cc_final: 0.6304 (tpt) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.7311 time to fit residues: 26.7175 Evaluate side-chains 34 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.0270 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107200 restraints weight = 2095.291| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.76 r_work: 0.3361 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1953 Z= 0.094 Angle : 0.473 3.947 2658 Z= 0.257 Chirality : 0.048 0.128 315 Planarity : 0.003 0.025 321 Dihedral : 4.600 18.775 264 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 24.29 % Favored : 73.81 % 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 are not related in a simple way. whole: -2.45 (0.53), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 104 TYR 0.016 0.001 TYR A 114 PHE 0.004 0.001 PHE C 87 TRP 0.003 0.001 TRP C 79 HIS 0.001 0.000 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.09 ( 1953) covalent geometry : angle 0.47329 / 0.26 ( 2658) hydrogen bonds : bond 0.02221 / 1.51 ( 32) hydrogen bonds : angle 4.93908 / 3.56 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: C 13 MET cc_start: 0.6789 (ttm) cc_final: 0.6428 (tpt) outliers start: 4 outliers final: 0 residues processed: 36 average time/residue: 0.7264 time to fit residues: 26.5528 Evaluate side-chains 33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105375 restraints weight = 2215.090| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.82 r_work: 0.3362 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1953 Z= 0.105 Angle : 0.478 3.583 2658 Z= 0.262 Chirality : 0.048 0.130 315 Planarity : 0.004 0.030 321 Dihedral : 4.623 18.815 264 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.38 % Allowed : 24.76 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.54), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 104 TYR 0.017 0.001 TYR A 114 PHE 0.005 0.001 PHE C 87 TRP 0.002 0.001 TRP C 79 HIS 0.002 0.000 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.10 ( 1953) covalent geometry : angle 0.47761 / 0.26 ( 2658) hydrogen bonds : bond 0.02255 / 1.52 ( 32) hydrogen bonds : angle 4.85850 / 3.51 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: C 13 MET cc_start: 0.6841 (ttm) cc_final: 0.6423 (tpt) outliers start: 5 outliers final: 1 residues processed: 36 average time/residue: 0.6952 time to fit residues: 25.4164 Evaluate side-chains 34 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106755 restraints weight = 2178.902| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.81 r_work: 0.3380 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1953 Z= 0.099 Angle : 0.467 3.547 2658 Z= 0.257 Chirality : 0.048 0.128 315 Planarity : 0.004 0.031 321 Dihedral : 4.569 18.772 264 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.95 % Allowed : 26.67 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.54), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 104 TYR 0.016 0.001 TYR A 114 PHE 0.005 0.001 PHE C 87 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.000 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 ( 1953) covalent geometry : angle 0.46711 / 0.26 ( 2658) hydrogen bonds : bond 0.02152 / 1.45 ( 32) hydrogen bonds : angle 4.80802 / 3.48 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: C 13 MET cc_start: 0.6789 (ttm) cc_final: 0.6396 (tpt) REVERT: C 15 LYS cc_start: 0.8149 (mttt) cc_final: 0.7689 (mtmt) outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 0.7452 time to fit residues: 27.2393 Evaluate side-chains 33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.125217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.101877 restraints weight = 2202.342| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.83 r_work: 0.3300 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1953 Z= 0.164 Angle : 0.534 3.625 2658 Z= 0.296 Chirality : 0.048 0.134 315 Planarity : 0.004 0.033 321 Dihedral : 4.922 20.474 264 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.95 % Allowed : 26.67 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.53), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 104 TYR 0.019 0.002 TYR A 114 PHE 0.007 0.002 PHE C 87 TRP 0.004 0.001 TRP A 79 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.16 ( 1953) covalent geometry : angle 0.53350 / 0.30 ( 2658) hydrogen bonds : bond 0.02709 / 1.74 ( 32) hydrogen bonds : angle 5.08287 / 3.65 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.079 Fit side-chains REVERT: B 13 MET cc_start: 0.7457 (ttm) cc_final: 0.6927 (tpt) REVERT: C 13 MET cc_start: 0.6819 (ttm) cc_final: 0.6399 (tpt) outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.7172 time to fit residues: 24.7532 Evaluate side-chains 33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.123396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100219 restraints weight = 2249.467| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.83 r_work: 0.3284 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1953 Z= 0.182 Angle : 0.560 3.762 2658 Z= 0.310 Chirality : 0.049 0.135 315 Planarity : 0.004 0.025 321 Dihedral : 5.057 20.892 264 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.95 % Allowed : 26.19 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.53), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 104 TYR 0.019 0.002 TYR A 114 PHE 0.008 0.002 PHE A 87 TRP 0.004 0.002 TRP A 79 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 ( 1953) covalent geometry : angle 0.56016 / 0.31 ( 2658) hydrogen bonds : bond 0.02856 / 1.81 ( 32) hydrogen bonds : angle 5.16865 / 3.70 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.076 Fit side-chains REVERT: B 13 MET cc_start: 0.7471 (ttm) cc_final: 0.6953 (tpt) REVERT: C 13 MET cc_start: 0.6819 (ttm) cc_final: 0.6403 (tpt) outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.6346 time to fit residues: 21.9125 Evaluate side-chains 33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105899 restraints weight = 2187.281| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.83 r_work: 0.3365 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1953 Z= 0.097 Angle : 0.473 3.584 2658 Z= 0.259 Chirality : 0.048 0.129 315 Planarity : 0.003 0.026 321 Dihedral : 4.662 19.054 264 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.43 % Allowed : 25.71 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.54), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 104 TYR 0.016 0.001 TYR B 114 PHE 0.004 0.001 PHE A 87 TRP 0.002 0.001 TRP C 79 HIS 0.001 0.000 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 1953) covalent geometry : angle 0.47321 / 0.26 ( 2658) hydrogen bonds : bond 0.02252 / 1.52 ( 32) hydrogen bonds : angle 4.85203 / 3.51 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.046 Fit side-chains REVERT: C 13 MET cc_start: 0.6803 (ttm) cc_final: 0.6350 (tpt) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 0.4921 time to fit residues: 17.4700 Evaluate side-chains 33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103295 restraints weight = 2265.191| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.86 r_work: 0.3336 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1953 Z= 0.122 Angle : 0.497 3.542 2658 Z= 0.274 Chirality : 0.048 0.132 315 Planarity : 0.004 0.037 321 Dihedral : 4.786 19.514 264 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.48 % Allowed : 27.62 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.54), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.019 0.002 TYR A 114 PHE 0.006 0.001 PHE C 87 TRP 0.002 0.001 TRP B 79 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 ( 1953) covalent geometry : angle 0.49664 / 0.27 ( 2658) hydrogen bonds : bond 0.02420 / 1.61 ( 32) hydrogen bonds : angle 4.92297 / 3.55 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 462 Ramachandran restraints generated. 231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.046 Fit side-chains revert: symmetry clash REVERT: C 13 MET cc_start: 0.6842 (ttm) cc_final: 0.6332 (tpt) outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.4684 time to fit residues: 15.2145 Evaluate side-chains 32 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102238 restraints weight = 2241.168| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.85 r_work: 0.3312 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1953 Z= 0.139 Angle : 0.518 3.696 2658 Z= 0.286 Chirality : 0.048 0.134 315 Planarity : 0.004 0.036 321 Dihedral : 4.900 19.914 264 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.48 % Allowed : 27.62 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.54), residues: 231 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.018 0.002 TYR A 114 PHE 0.006 0.001 PHE C 87 TRP 0.003 0.001 TRP B 79 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 1953) covalent geometry : angle 0.51838 / 0.29 ( 2658) hydrogen bonds : bond 0.02566 / 1.68 ( 32) hydrogen bonds : angle 5.00496 / 3.61 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 943.51 seconds wall clock time: 16 minutes 58.51 seconds (1018.51 seconds total)