Starting phenix.real_space_refine on Tue Mar 3 10:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l4s_0833/03_2026/6l4s_0833.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l4s_0833/03_2026/6l4s_0833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6l4s_0833/03_2026/6l4s_0833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l4s_0833/03_2026/6l4s_0833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l4s_0833/03_2026/6l4s_0833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l4s_0833/03_2026/6l4s_0833.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 1410 2.51 5 N 408 2.21 5 O 450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.41, per 1000 atoms: 0.18 Number of scatterers: 2268 At special positions: 0 Unit cell: (83.79, 91.77, 35.91, 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 450 8.00 N 408 7.00 C 1410 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 95.6 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 48 removed outlier: 6.361A pdb=" N GLY A 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.156A pdb=" N GLU A 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR E 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.585A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 78 removed outlier: 6.275A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 93 removed outlier: 6.831A pdb=" N THR C 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR A 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 removed outlier: 6.552A pdb=" N GLY B 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 removed outlier: 6.327A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.438A pdb=" N VAL B 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.474A pdb=" N THR B 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA D 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.880A pdb=" N THR D 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR B 92 " --> pdb=" O GLY F 93 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 54 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: 0.27 Time building geometry restraints manager: 0.23 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: 402 1.28 - 1.35: 360 1.35 - 1.42: 60 1.42 - 1.49: 538 1.49 - 1.56: 914 Bond restraints: 2274 Sorted by residual: bond pdb=" CB VAL E 74 " pdb=" CG1 VAL E 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB VAL D 74 " pdb=" CG1 VAL D 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB VAL A 74 " pdb=" CG1 VAL A 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.46e+00 bond pdb=" CB VAL F 74 " pdb=" CG1 VAL F 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.45e+00 bond pdb=" CB VAL C 74 " pdb=" CG1 VAL C 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.45e+00 ... (remaining 2269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 2626 1.67 - 3.34: 326 3.34 - 5.01: 96 5.01 - 6.68: 12 6.68 - 8.35: 6 Bond angle restraints: 3066 Sorted by residual: angle pdb=" C VAL C 66 " pdb=" N GLY C 67 " pdb=" CA GLY C 67 " ideal model delta sigma weight residual 121.41 113.06 8.35 1.96e+00 2.60e-01 1.81e+01 angle pdb=" C VAL F 66 " pdb=" N GLY F 67 " pdb=" CA GLY F 67 " ideal model delta sigma weight residual 121.41 113.08 8.33 1.96e+00 2.60e-01 1.81e+01 angle pdb=" C VAL D 66 " pdb=" N GLY D 67 " pdb=" CA GLY D 67 " ideal model delta sigma weight residual 121.41 113.10 8.31 1.96e+00 2.60e-01 1.80e+01 angle pdb=" C VAL A 66 " pdb=" N GLY A 67 " pdb=" CA GLY A 67 " ideal model delta sigma weight residual 121.41 113.11 8.30 1.96e+00 2.60e-01 1.79e+01 angle pdb=" C VAL B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta sigma weight residual 121.41 113.12 8.29 1.96e+00 2.60e-01 1.79e+01 ... (remaining 3061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.36: 1020 7.36 - 14.71: 222 14.71 - 22.07: 78 22.07 - 29.42: 12 29.42 - 36.78: 12 Dihedral angle restraints: 1344 sinusoidal: 456 harmonic: 888 Sorted by residual: dihedral pdb=" CA GLY C 93 " pdb=" C GLY C 93 " pdb=" N PHE C 94 " pdb=" CA PHE C 94 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY E 93 " pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY D 93 " pdb=" C GLY D 93 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 1341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 289 0.087 - 0.175: 101 0.175 - 0.262: 6 0.262 - 0.349: 0 0.349 - 0.436: 6 Chirality restraints: 402 Sorted by residual: chirality pdb=" CB VAL E 95 " pdb=" CA VAL E 95 " pdb=" CG1 VAL E 95 " pdb=" CG2 VAL E 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CB VAL F 95 " pdb=" CA VAL F 95 " pdb=" CG1 VAL F 95 " pdb=" CG2 VAL F 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CB VAL D 95 " pdb=" CA VAL D 95 " pdb=" CG1 VAL D 95 " pdb=" CG2 VAL D 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.74e+00 ... (remaining 399 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 52 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" C VAL C 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL C 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 53 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 52 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C VAL B 52 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL B 52 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 52 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C VAL A 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL A 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 53 " 0.013 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 961 2.91 - 3.40: 1874 3.40 - 3.90: 3350 3.90 - 4.40: 3778 4.40 - 4.90: 7475 Nonbonded interactions: 17438 Sorted by model distance: nonbonded pdb=" OG1 THR A 54 " pdb=" OG1 THR E 64 " model vdw 2.408 3.040 nonbonded pdb=" OG1 THR B 54 " pdb=" OG1 THR F 64 " model vdw 2.459 3.040 nonbonded pdb=" OG1 THR B 64 " pdb=" OG1 THR D 54 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP A 98 " pdb=" N GLN A 99 " model vdw 2.524 3.120 nonbonded pdb=" OD1 ASP F 98 " pdb=" N GLN F 99 " model vdw 2.524 3.120 ... (remaining 17433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.250 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 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 : 0.014 0.070 2274 Z= 0.642 Angle : 1.363 8.347 3066 Z= 0.791 Chirality : 0.091 0.436 402 Planarity : 0.006 0.023 384 Dihedral : 10.279 36.779 780 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.73 (0.35), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.27), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.007 PHE A 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.01401 ( 2274) covalent geometry : angle 1.36312 ( 3066) hydrogen bonds : bond 0.21303 ( 19) hydrogen bonds : angle 8.26716 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.086 Fit side-chains REVERT: A 57 GLU cc_start: 0.7206 (tt0) cc_final: 0.6883 (tm-30) REVERT: A 58 LYS cc_start: 0.7161 (mmtp) cc_final: 0.6738 (tptm) REVERT: A 62 GLN cc_start: 0.8097 (mt0) cc_final: 0.7744 (mt0) REVERT: A 83 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7756 (mp0) REVERT: A 97 LYS cc_start: 0.7233 (mmtt) cc_final: 0.7028 (mmtm) REVERT: B 57 GLU cc_start: 0.7007 (tt0) cc_final: 0.6717 (tm-30) REVERT: B 58 LYS cc_start: 0.7282 (mmtp) cc_final: 0.6721 (mmtt) REVERT: B 62 GLN cc_start: 0.7760 (mt0) cc_final: 0.7266 (mt0) REVERT: B 64 THR cc_start: 0.7587 (m) cc_final: 0.7323 (m) REVERT: B 97 LYS cc_start: 0.7664 (mmtt) cc_final: 0.7125 (mmtt) REVERT: C 57 GLU cc_start: 0.7398 (tt0) cc_final: 0.7084 (tm-30) REVERT: C 58 LYS cc_start: 0.8372 (mmtp) cc_final: 0.8151 (mmtt) REVERT: C 97 LYS cc_start: 0.8343 (mmtt) cc_final: 0.6588 (mtmt) REVERT: D 57 GLU cc_start: 0.7498 (tt0) cc_final: 0.6755 (tm-30) REVERT: D 58 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7518 (mmmt) REVERT: D 62 GLN cc_start: 0.7601 (mt0) cc_final: 0.7329 (mt0) REVERT: D 97 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7916 (mmtt) REVERT: E 57 GLU cc_start: 0.8203 (tt0) cc_final: 0.7890 (tm-30) REVERT: E 58 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7503 (mmtt) REVERT: E 83 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7575 (pm20) REVERT: F 57 GLU cc_start: 0.7885 (tt0) cc_final: 0.7412 (tm-30) REVERT: F 58 LYS cc_start: 0.7218 (mmtp) cc_final: 0.6507 (mmmt) REVERT: F 97 LYS cc_start: 0.6886 (mmtt) cc_final: 0.6606 (mmtm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1023 time to fit residues: 8.6917 Evaluate side-chains 77 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** 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 = 0.4678 r_free = 0.4678 target = 0.185197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.142122 restraints weight = 2445.396| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.95 r_work: 0.4112 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2274 Z= 0.129 Angle : 0.570 4.400 3066 Z= 0.315 Chirality : 0.052 0.150 402 Planarity : 0.002 0.016 384 Dihedral : 5.939 16.898 324 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.63 % Allowed : 20.18 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.25 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE B 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2274) covalent geometry : angle 0.56986 ( 3066) hydrogen bonds : bond 0.01171 ( 19) hydrogen bonds : angle 5.71605 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.085 Fit side-chains REVERT: A 57 GLU cc_start: 0.7989 (tt0) cc_final: 0.7572 (tm-30) REVERT: A 58 LYS cc_start: 0.7787 (mmtp) cc_final: 0.7195 (tptm) REVERT: A 60 LYS cc_start: 0.8484 (mptt) cc_final: 0.8226 (mmtp) REVERT: A 96 LYS cc_start: 0.7966 (mtpm) cc_final: 0.7607 (mtmt) REVERT: A 97 LYS cc_start: 0.7840 (mmtt) cc_final: 0.7620 (mmtp) REVERT: B 57 GLU cc_start: 0.7629 (tt0) cc_final: 0.7113 (tm-30) REVERT: B 58 LYS cc_start: 0.7900 (mmtp) cc_final: 0.7663 (tttt) REVERT: B 97 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7676 (mmtt) REVERT: C 57 GLU cc_start: 0.7908 (tt0) cc_final: 0.7590 (tm-30) REVERT: D 57 GLU cc_start: 0.7942 (tt0) cc_final: 0.7532 (tm-30) REVERT: D 96 LYS cc_start: 0.8053 (mtpm) cc_final: 0.7213 (mttt) REVERT: E 60 LYS cc_start: 0.8707 (tptt) cc_final: 0.8370 (mmtp) REVERT: E 62 GLN cc_start: 0.7272 (mt0) cc_final: 0.7038 (mt0) REVERT: F 45 LYS cc_start: 0.5550 (mmtt) cc_final: 0.5246 (mmtm) REVERT: F 57 GLU cc_start: 0.8247 (tt0) cc_final: 0.7613 (tm-30) REVERT: F 58 LYS cc_start: 0.7993 (mmtp) cc_final: 0.7072 (mmmt) REVERT: F 59 THR cc_start: 0.8688 (m) cc_final: 0.8347 (t) REVERT: F 62 GLN cc_start: 0.7647 (mt0) cc_final: 0.7028 (mt0) REVERT: F 97 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7177 (mmtm) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 0.1007 time to fit residues: 8.2570 Evaluate side-chains 68 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** 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 = 0.4486 r_free = 0.4486 target = 0.167452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.124946 restraints weight = 2579.443| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 3.80 r_work: 0.3957 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 2274 Z= 0.397 Angle : 0.765 5.581 3066 Z= 0.428 Chirality : 0.056 0.164 402 Planarity : 0.004 0.014 384 Dihedral : 6.952 19.781 324 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 7.02 % Allowed : 21.05 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.89 (0.35), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.27), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE A 94 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00828 ( 2274) covalent geometry : angle 0.76476 ( 3066) hydrogen bonds : bond 0.02229 ( 19) hydrogen bonds : angle 5.56411 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.087 Fit side-chains REVERT: A 57 GLU cc_start: 0.8145 (tt0) cc_final: 0.7566 (tm-30) REVERT: A 58 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7565 (tptm) REVERT: B 57 GLU cc_start: 0.7824 (tt0) cc_final: 0.7180 (tm-30) REVERT: C 57 GLU cc_start: 0.7800 (tt0) cc_final: 0.7540 (tm-30) REVERT: D 57 GLU cc_start: 0.8017 (tt0) cc_final: 0.7592 (tm-30) REVERT: F 45 LYS cc_start: 0.4930 (mmtt) cc_final: 0.4699 (mmtm) REVERT: F 57 GLU cc_start: 0.8252 (tt0) cc_final: 0.7806 (tm-30) REVERT: F 58 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7480 (mmtp) REVERT: F 59 THR cc_start: 0.8574 (m) cc_final: 0.8226 (t) REVERT: F 97 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7881 (mmtm) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.0870 time to fit residues: 8.5960 Evaluate side-chains 88 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.173923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.133324 restraints weight = 2522.769| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.84 r_work: 0.3970 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2274 Z= 0.247 Angle : 0.628 5.092 3066 Z= 0.348 Chirality : 0.054 0.156 402 Planarity : 0.002 0.011 384 Dihedral : 6.182 17.941 324 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 8.33 % Allowed : 22.81 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.94 (0.36), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.27), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE A 94 HIS 0.001 0.000 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 2274) covalent geometry : angle 0.62818 ( 3066) hydrogen bonds : bond 0.01718 ( 19) hydrogen bonds : angle 5.15152 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.086 Fit side-chains REVERT: A 57 GLU cc_start: 0.8227 (tt0) cc_final: 0.7540 (tm-30) REVERT: A 58 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7477 (tptm) REVERT: A 60 LYS cc_start: 0.8464 (mptt) cc_final: 0.8194 (mptt) REVERT: B 57 GLU cc_start: 0.7824 (tt0) cc_final: 0.7258 (tm-30) REVERT: D 57 GLU cc_start: 0.8022 (tt0) cc_final: 0.7780 (tm-30) REVERT: E 62 GLN cc_start: 0.7388 (mt0) cc_final: 0.7089 (mt0) REVERT: F 57 GLU cc_start: 0.8363 (tt0) cc_final: 0.7695 (tm-30) REVERT: F 58 LYS cc_start: 0.8152 (mmtp) cc_final: 0.7199 (mmmt) REVERT: F 59 THR cc_start: 0.8689 (m) cc_final: 0.8441 (t) REVERT: F 62 GLN cc_start: 0.7686 (mt0) cc_final: 0.7420 (mt0) outliers start: 19 outliers final: 16 residues processed: 84 average time/residue: 0.0835 time to fit residues: 7.9009 Evaluate side-chains 88 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 20.0000 chunk 24 optimal weight: 0.0010 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 overall best weight: 3.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.174603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.133946 restraints weight = 2494.445| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 3.82 r_work: 0.4014 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2274 Z= 0.212 Angle : 0.606 5.096 3066 Z= 0.332 Chirality : 0.053 0.150 402 Planarity : 0.002 0.010 384 Dihedral : 5.862 17.590 324 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 9.21 % Allowed : 20.18 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.86 (0.36), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 94 HIS 0.001 0.000 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 2274) covalent geometry : angle 0.60604 ( 3066) hydrogen bonds : bond 0.01471 ( 19) hydrogen bonds : angle 4.93677 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.097 Fit side-chains REVERT: A 57 GLU cc_start: 0.8116 (tt0) cc_final: 0.7444 (tm-30) REVERT: A 58 LYS cc_start: 0.7764 (mmtp) cc_final: 0.7021 (mmmt) REVERT: A 60 LYS cc_start: 0.8397 (mptt) cc_final: 0.8161 (mptt) REVERT: A 97 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8074 (mmtm) REVERT: B 57 GLU cc_start: 0.7820 (tt0) cc_final: 0.7258 (tm-30) REVERT: B 58 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7413 (mttt) REVERT: C 57 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6958 (tm-30) REVERT: D 45 LYS cc_start: 0.2935 (tptt) cc_final: 0.2715 (tptp) REVERT: D 98 ASP cc_start: 0.6388 (t0) cc_final: 0.6143 (t0) REVERT: E 83 GLU cc_start: 0.8192 (mp0) cc_final: 0.7838 (mp0) REVERT: F 57 GLU cc_start: 0.8325 (tt0) cc_final: 0.7695 (tm-30) REVERT: F 58 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7217 (mmmt) REVERT: F 62 GLN cc_start: 0.7664 (mt0) cc_final: 0.7384 (mt0) REVERT: F 97 LYS cc_start: 0.8367 (mmtp) cc_final: 0.8050 (mmtm) outliers start: 21 outliers final: 17 residues processed: 82 average time/residue: 0.0857 time to fit residues: 7.9192 Evaluate side-chains 86 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 25 optimal weight: 0.0470 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.6084 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.176128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.135840 restraints weight = 2474.589| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.81 r_work: 0.3995 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2274 Z= 0.193 Angle : 0.567 4.959 3066 Z= 0.311 Chirality : 0.053 0.148 402 Planarity : 0.002 0.009 384 Dihedral : 5.603 16.712 324 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 8.33 % Allowed : 20.61 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.77 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 94 HIS 0.001 0.000 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 2274) covalent geometry : angle 0.56664 ( 3066) hydrogen bonds : bond 0.01392 ( 19) hydrogen bonds : angle 4.72241 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.082 Fit side-chains REVERT: A 57 GLU cc_start: 0.8159 (tt0) cc_final: 0.7549 (tm-30) REVERT: A 58 LYS cc_start: 0.7851 (mmtp) cc_final: 0.7138 (mmmt) REVERT: A 60 LYS cc_start: 0.8470 (mptt) cc_final: 0.8240 (mptt) REVERT: B 57 GLU cc_start: 0.8011 (tt0) cc_final: 0.7338 (tm-30) REVERT: B 58 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7430 (mttt) REVERT: C 57 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7271 (tm-30) REVERT: D 57 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7481 (tm-30) REVERT: D 83 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7949 (mt-10) REVERT: E 62 GLN cc_start: 0.7507 (mt0) cc_final: 0.7153 (mt0) REVERT: E 83 GLU cc_start: 0.8224 (mp0) cc_final: 0.7855 (mp0) REVERT: F 57 GLU cc_start: 0.8425 (tt0) cc_final: 0.7671 (tm-30) outliers start: 19 outliers final: 16 residues processed: 78 average time/residue: 0.0856 time to fit residues: 7.4702 Evaluate side-chains 81 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 0.0000 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 20 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.8990 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.175605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.135597 restraints weight = 2492.574| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 3.82 r_work: 0.4023 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2274 Z= 0.206 Angle : 0.582 5.226 3066 Z= 0.318 Chirality : 0.053 0.146 402 Planarity : 0.002 0.008 384 Dihedral : 5.591 16.674 324 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 8.33 % Allowed : 19.74 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.72 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 94 HIS 0.001 0.000 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 2274) covalent geometry : angle 0.58199 ( 3066) hydrogen bonds : bond 0.01422 ( 19) hydrogen bonds : angle 4.67965 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.074 Fit side-chains REVERT: A 45 LYS cc_start: 0.5459 (mmtt) cc_final: 0.5121 (mmtt) REVERT: A 57 GLU cc_start: 0.8020 (tt0) cc_final: 0.7290 (tm-30) REVERT: A 58 LYS cc_start: 0.7691 (mmtp) cc_final: 0.7275 (mmmt) REVERT: A 60 LYS cc_start: 0.8378 (mptt) cc_final: 0.8153 (mptt) REVERT: A 97 LYS cc_start: 0.8256 (mmtt) cc_final: 0.8029 (mmtt) REVERT: B 57 GLU cc_start: 0.7748 (tt0) cc_final: 0.7128 (tm-30) REVERT: B 58 LYS cc_start: 0.7763 (mmtp) cc_final: 0.7348 (mttt) REVERT: C 57 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7046 (tm-30) REVERT: D 57 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7361 (tm-30) REVERT: D 83 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7945 (mt-10) REVERT: D 98 ASP cc_start: 0.6483 (t0) cc_final: 0.6276 (t0) REVERT: E 62 GLN cc_start: 0.7523 (mt0) cc_final: 0.7130 (mt0) REVERT: E 83 GLU cc_start: 0.8231 (mp0) cc_final: 0.7824 (mp0) REVERT: F 57 GLU cc_start: 0.8433 (tt0) cc_final: 0.7600 (tm-30) REVERT: F 58 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7099 (mmmt) REVERT: F 97 LYS cc_start: 0.8258 (mmtp) cc_final: 0.7883 (mmtm) outliers start: 19 outliers final: 17 residues processed: 77 average time/residue: 0.0848 time to fit residues: 7.2658 Evaluate side-chains 83 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.173288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.133792 restraints weight = 2583.074| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.68 r_work: 0.3978 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 2274 Z= 0.375 Angle : 0.737 5.627 3066 Z= 0.409 Chirality : 0.059 0.176 402 Planarity : 0.003 0.008 384 Dihedral : 6.325 18.792 324 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 8.77 % Allowed : 20.61 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.04 (0.36), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE D 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00784 ( 2274) covalent geometry : angle 0.73692 ( 3066) hydrogen bonds : bond 0.01625 ( 19) hydrogen bonds : angle 4.99471 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.082 Fit side-chains REVERT: A 45 LYS cc_start: 0.5823 (mmtt) cc_final: 0.5611 (mmtt) REVERT: A 57 GLU cc_start: 0.8178 (tt0) cc_final: 0.7430 (tm-30) REVERT: A 58 LYS cc_start: 0.7979 (mmtp) cc_final: 0.7595 (mmtp) REVERT: A 97 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8170 (mmtm) REVERT: B 57 GLU cc_start: 0.7971 (tt0) cc_final: 0.7334 (tm-30) REVERT: C 57 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7207 (tm-30) REVERT: D 57 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7589 (tm-30) REVERT: D 83 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8011 (mt-10) REVERT: E 57 GLU cc_start: 0.8360 (tt0) cc_final: 0.8133 (tm-30) REVERT: E 62 GLN cc_start: 0.7469 (mt0) cc_final: 0.7152 (mt0) REVERT: F 57 GLU cc_start: 0.8366 (tt0) cc_final: 0.7895 (tm-30) REVERT: F 58 LYS cc_start: 0.8240 (mmtp) cc_final: 0.7296 (mmmt) outliers start: 20 outliers final: 17 residues processed: 89 average time/residue: 0.0624 time to fit residues: 6.3834 Evaluate side-chains 97 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4626 r_free = 0.4626 target = 0.181452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.140760 restraints weight = 2541.483| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 3.86 r_work: 0.4072 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2274 Z= 0.152 Angle : 0.574 5.532 3066 Z= 0.310 Chirality : 0.054 0.153 402 Planarity : 0.002 0.008 384 Dihedral : 5.377 15.658 324 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.58 % Allowed : 22.81 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.76 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 94 HIS 0.001 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2274) covalent geometry : angle 0.57390 ( 3066) hydrogen bonds : bond 0.01185 ( 19) hydrogen bonds : angle 4.65026 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.079 Fit side-chains REVERT: A 57 GLU cc_start: 0.8156 (tt0) cc_final: 0.7446 (tm-30) REVERT: A 58 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7477 (mmmt) REVERT: B 45 LYS cc_start: 0.5163 (mmtt) cc_final: 0.4741 (mmtt) REVERT: B 57 GLU cc_start: 0.7979 (tt0) cc_final: 0.7305 (tm-30) REVERT: B 58 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7434 (mttt) REVERT: C 57 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7345 (tm-30) REVERT: C 58 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8121 (mmtt) REVERT: D 57 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7621 (tm-30) REVERT: D 83 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7941 (mt-10) REVERT: E 62 GLN cc_start: 0.7518 (mt0) cc_final: 0.7168 (mt0) REVERT: F 57 GLU cc_start: 0.8369 (tt0) cc_final: 0.7625 (tm-30) outliers start: 15 outliers final: 13 residues processed: 76 average time/residue: 0.0708 time to fit residues: 6.1568 Evaluate side-chains 80 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.175917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.135829 restraints weight = 2607.207| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 3.75 r_work: 0.3947 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2274 Z= 0.277 Angle : 0.700 6.196 3066 Z= 0.379 Chirality : 0.055 0.148 402 Planarity : 0.002 0.009 384 Dihedral : 5.858 17.562 324 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 7.02 % Allowed : 23.25 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.83 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE D 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 2274) covalent geometry : angle 0.69971 ( 3066) hydrogen bonds : bond 0.01572 ( 19) hydrogen bonds : angle 4.75056 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.058 Fit side-chains REVERT: A 57 GLU cc_start: 0.8119 (tt0) cc_final: 0.7377 (tm-30) REVERT: A 58 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7622 (mmtp) REVERT: B 45 LYS cc_start: 0.5266 (mmtt) cc_final: 0.4862 (mmtt) REVERT: B 57 GLU cc_start: 0.7906 (tt0) cc_final: 0.7270 (tm-30) REVERT: C 57 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7203 (tm-30) REVERT: D 57 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 83 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7987 (mt-10) REVERT: E 62 GLN cc_start: 0.7509 (mt0) cc_final: 0.7166 (mt0) REVERT: F 57 GLU cc_start: 0.8324 (tt0) cc_final: 0.7931 (tm-30) REVERT: F 58 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7272 (mmmt) outliers start: 16 outliers final: 14 residues processed: 78 average time/residue: 0.0575 time to fit residues: 5.1215 Evaluate side-chains 85 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 0.0770 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- 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 = 0.4778 r_free = 0.4778 target = 0.192402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.154403 restraints weight = 2427.177| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 3.67 r_work: 0.4173 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2274 Z= 0.124 Angle : 0.608 7.507 3066 Z= 0.322 Chirality : 0.052 0.145 402 Planarity : 0.002 0.014 384 Dihedral : 5.094 14.952 324 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.14 % Allowed : 24.56 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.61 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2274) covalent geometry : angle 0.60796 ( 3066) hydrogen bonds : bond 0.01064 ( 19) hydrogen bonds : angle 4.42222 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 824.84 seconds wall clock time: 14 minutes 42.21 seconds (882.21 seconds total)