Starting phenix.real_space_refine on Mon Feb 10 20:24:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l4s_0833/02_2025/6l4s_0833.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l4s_0833/02_2025/6l4s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6l4s_0833/02_2025/6l4s_0833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l4s_0833/02_2025/6l4s_0833.map" model { file = "/net/cci-nas-00/data/ceres_data/6l4s_0833/02_2025/6l4s_0833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l4s_0833/02_2025/6l4s_0833.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, F Time building chain proxies: 1.25, per 1000 atoms: 0.55 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: 0.56 Conformation dependent library (CDL) restraints added in 307.1 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: 0.30 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: 0.45 Time building geometry restraints manager: 0.63 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.000 Normalize map: mean=0, sd=1: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.820 Find NCS groups from input model: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- 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= 0.956 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS D 50 PHE 0.015 0.007 PHE A 94 *********************** 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 : 0.235 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: 0.7745 (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: 0.7588 (m) cc_final: 0.7323 (m) REVERT: B 97 LYS cc_start: 0.7663 (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: 0.8257 (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: 0.7886 (tt0) cc_final: 0.7412 (tm-30) REVERT: F 58 LYS cc_start: 0.7217 (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: 0.2256 time to fit residues: 19.1161 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 : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.176344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.133864 restraints weight = 2487.235| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.92 r_work: 0.4012 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2274 Z= 0.263 Angle : 0.614 4.492 3066 Z= 0.340 Chirality : 0.052 0.156 402 Planarity : 0.002 0.015 384 Dihedral : 6.341 17.530 324 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.51 % Allowed : 19.74 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.36), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.009 0.002 PHE B 94 *********************** 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 78 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.213 Fit side-chains REVERT: A 57 GLU cc_start: 0.8008 (tt0) cc_final: 0.7549 (tm-30) REVERT: A 58 LYS cc_start: 0.7817 (mmtp) cc_final: 0.7207 (tptm) REVERT: A 60 LYS cc_start: 0.8529 (mptt) cc_final: 0.8278 (mmtp) REVERT: B 57 GLU cc_start: 0.7730 (tt0) cc_final: 0.7147 (tm-30) REVERT: B 58 LYS cc_start: 0.7929 (mmtp) cc_final: 0.7585 (mttt) REVERT: B 97 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7675 (mmtt) REVERT: C 57 GLU cc_start: 0.7852 (tt0) cc_final: 0.7514 (tm-30) REVERT: D 57 GLU cc_start: 0.7988 (tt0) cc_final: 0.7547 (tm-30) REVERT: E 55 VAL cc_start: 0.8695 (t) cc_final: 0.8487 (t) REVERT: E 60 LYS cc_start: 0.8687 (tptt) cc_final: 0.8426 (mptt) REVERT: F 45 LYS cc_start: 0.5399 (mmtt) cc_final: 0.5089 (mmtm) REVERT: F 57 GLU cc_start: 0.8255 (tt0) cc_final: 0.7637 (tm-30) REVERT: F 58 LYS cc_start: 0.8016 (mmtp) cc_final: 0.7013 (mmmt) REVERT: F 59 THR cc_start: 0.8627 (m) cc_final: 0.8259 (t) REVERT: F 62 GLN cc_start: 0.7532 (mt0) cc_final: 0.7045 (mt0) REVERT: F 97 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7474 (mmtm) outliers start: 8 outliers final: 8 residues processed: 75 average time/residue: 0.2135 time to fit residues: 17.6861 Evaluate side-chains 71 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 0.3980 chunk 15 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4757 r_free = 0.4757 target = 0.190565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.147294 restraints weight = 2357.593| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 3.89 r_work: 0.4230 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2274 Z= 0.143 Angle : 0.495 4.127 3066 Z= 0.273 Chirality : 0.051 0.144 402 Planarity : 0.002 0.012 384 Dihedral : 5.233 15.128 324 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.19 % Allowed : 26.32 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.006 0.001 PHE F 94 *********************** 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 64 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.261 Fit side-chains REVERT: A 57 GLU cc_start: 0.8086 (tt0) cc_final: 0.7778 (tm-30) REVERT: A 58 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7954 (tptt) REVERT: A 60 LYS cc_start: 0.8543 (mptt) cc_final: 0.8057 (mmtp) REVERT: B 58 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7414 (mmmm) REVERT: C 57 GLU cc_start: 0.7910 (tt0) cc_final: 0.7708 (tm-30) REVERT: C 58 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8099 (mmtt) REVERT: C 97 LYS cc_start: 0.8050 (mmtp) cc_final: 0.5102 (ptpt) REVERT: D 57 GLU cc_start: 0.7957 (tt0) cc_final: 0.7630 (tm-30) REVERT: D 58 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7583 (mmmt) REVERT: D 96 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7624 (mttt) REVERT: D 97 LYS cc_start: 0.8037 (mmtp) cc_final: 0.5015 (ptpt) REVERT: F 62 GLN cc_start: 0.7634 (mt0) cc_final: 0.7149 (mt0) REVERT: F 97 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7884 (mmtm) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.2214 time to fit residues: 15.0037 Evaluate side-chains 60 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 59 THR 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 11 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.172244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.128560 restraints weight = 2447.457| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.89 r_work: 0.3992 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2274 Z= 0.346 Angle : 0.586 4.429 3066 Z= 0.325 Chirality : 0.052 0.152 402 Planarity : 0.002 0.010 384 Dihedral : 5.922 17.133 324 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.14 % Allowed : 22.37 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.005 0.001 PHE A 94 *********************** 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 87 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.256 Fit side-chains REVERT: A 57 GLU cc_start: 0.8096 (tt0) cc_final: 0.7443 (tm-30) REVERT: A 58 LYS cc_start: 0.8053 (mmtp) cc_final: 0.7454 (tptm) REVERT: A 60 LYS cc_start: 0.8432 (mptt) cc_final: 0.8090 (mptt) REVERT: B 57 GLU cc_start: 0.7806 (tt0) cc_final: 0.7173 (tm-30) REVERT: C 57 GLU cc_start: 0.7815 (tt0) cc_final: 0.7512 (tm-30) REVERT: D 57 GLU cc_start: 0.7962 (tt0) cc_final: 0.7541 (tm-30) REVERT: D 97 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8132 (mmtt) REVERT: E 62 GLN cc_start: 0.7423 (mt0) cc_final: 0.7002 (mt0) REVERT: F 57 GLU cc_start: 0.8354 (tt0) cc_final: 0.7616 (tm-30) REVERT: F 58 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7097 (mmmt) REVERT: F 62 GLN cc_start: 0.7490 (mt0) cc_final: 0.7251 (mt0) outliers start: 14 outliers final: 13 residues processed: 78 average time/residue: 0.1855 time to fit residues: 16.3153 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 : 0.250 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain D residue 49 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 59 THR 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 28 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- 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 = 0.4548 r_free = 0.4548 target = 0.174510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.133261 restraints weight = 2474.463| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 3.74 r_work: 0.4003 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2274 Z= 0.391 Angle : 0.628 4.816 3066 Z= 0.348 Chirality : 0.054 0.156 402 Planarity : 0.002 0.009 384 Dihedral : 6.057 16.879 324 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 9.21 % Allowed : 24.56 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.005 0.001 PHE A 94 *********************** 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 94 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.245 Fit side-chains REVERT: A 57 GLU cc_start: 0.8181 (tt0) cc_final: 0.7466 (tm-30) REVERT: A 58 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7459 (tptm) REVERT: A 60 LYS cc_start: 0.8461 (mptt) cc_final: 0.8187 (mptt) REVERT: B 57 GLU cc_start: 0.7810 (tt0) cc_final: 0.7149 (tm-30) REVERT: D 57 GLU cc_start: 0.7956 (tt0) cc_final: 0.7621 (tm-30) REVERT: D 98 ASP cc_start: 0.6653 (t0) cc_final: 0.6385 (t0) REVERT: E 62 GLN cc_start: 0.7471 (mt0) cc_final: 0.7075 (mt0) REVERT: E 83 GLU cc_start: 0.8364 (mp0) cc_final: 0.8126 (mp0) REVERT: F 57 GLU cc_start: 0.8363 (tt0) cc_final: 0.7797 (tm-30) REVERT: F 58 LYS cc_start: 0.8053 (mmtp) cc_final: 0.7130 (mmmt) REVERT: F 97 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8081 (mmtm) outliers start: 21 outliers final: 18 residues processed: 80 average time/residue: 0.1911 time to fit residues: 17.1713 Evaluate side-chains 86 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 52 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 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 96 LYS 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 59 THR 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 2 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.174342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.134149 restraints weight = 2485.659| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 3.80 r_work: 0.4019 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3997 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= 0.342 Angle : 0.597 4.766 3066 Z= 0.329 Chirality : 0.053 0.153 402 Planarity : 0.002 0.009 384 Dihedral : 5.782 16.557 324 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 9.65 % Allowed : 21.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.004 0.001 PHE A 94 *********************** 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 95 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.258 Fit side-chains REVERT: A 57 GLU cc_start: 0.8123 (tt0) cc_final: 0.7459 (tm-30) REVERT: A 58 LYS cc_start: 0.7895 (mmtp) cc_final: 0.7406 (mmtp) REVERT: A 60 LYS cc_start: 0.8420 (mptt) cc_final: 0.8167 (mptt) REVERT: B 57 GLU cc_start: 0.7749 (tt0) cc_final: 0.7211 (tm-30) REVERT: C 57 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6963 (tm-30) REVERT: D 57 GLU cc_start: 0.7934 (tt0) cc_final: 0.7719 (tm-30) REVERT: D 83 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7919 (mt-10) REVERT: E 62 GLN cc_start: 0.7475 (mt0) cc_final: 0.7082 (mt0) REVERT: F 57 GLU cc_start: 0.8360 (tt0) cc_final: 0.7898 (tm-30) REVERT: F 58 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7196 (mmmt) outliers start: 22 outliers final: 18 residues processed: 80 average time/residue: 0.2196 time to fit residues: 19.7630 Evaluate side-chains 84 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.171669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.131466 restraints weight = 2545.408| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.73 r_work: 0.3969 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 2274 Z= 0.469 Angle : 0.686 5.156 3066 Z= 0.380 Chirality : 0.056 0.159 402 Planarity : 0.003 0.008 384 Dihedral : 6.244 17.629 324 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 9.65 % Allowed : 21.93 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.004 0.001 PHE A 94 *********************** 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 100 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.260 Fit side-chains REVERT: A 57 GLU cc_start: 0.8155 (tt0) cc_final: 0.7427 (tm-30) REVERT: A 58 LYS cc_start: 0.7969 (mmtp) cc_final: 0.7497 (mmtp) REVERT: A 60 LYS cc_start: 0.8451 (mptt) cc_final: 0.8249 (mptt) REVERT: B 57 GLU cc_start: 0.7913 (tt0) cc_final: 0.7372 (tm-30) REVERT: C 45 LYS cc_start: 0.3052 (tptp) cc_final: 0.2641 (tptp) REVERT: C 57 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7200 (tm-30) REVERT: D 83 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8004 (mt-10) REVERT: E 57 GLU cc_start: 0.8495 (tt0) cc_final: 0.8265 (tm-30) REVERT: E 62 GLN cc_start: 0.7502 (mt0) cc_final: 0.7277 (mt0) REVERT: F 57 GLU cc_start: 0.8345 (tt0) cc_final: 0.7861 (tm-30) REVERT: F 58 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7292 (mmmt) outliers start: 22 outliers final: 18 residues processed: 85 average time/residue: 0.1609 time to fit residues: 15.6062 Evaluate side-chains 91 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain C residue 95 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 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 6 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.4608 r_free = 0.4608 target = 0.178461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.138558 restraints weight = 2587.376| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.80 r_work: 0.4047 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4459 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= 0.221 Angle : 0.560 5.523 3066 Z= 0.304 Chirality : 0.053 0.149 402 Planarity : 0.002 0.009 384 Dihedral : 5.372 15.483 324 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.58 % Allowed : 23.25 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.006 0.001 PHE A 94 *********************** 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 85 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.193 Fit side-chains REVERT: A 57 GLU cc_start: 0.8149 (tt0) cc_final: 0.7538 (tm-30) REVERT: A 58 LYS cc_start: 0.7964 (mmtp) cc_final: 0.7548 (mmmt) REVERT: A 60 LYS cc_start: 0.8509 (mptt) cc_final: 0.8289 (mptt) REVERT: B 57 GLU cc_start: 0.8051 (tt0) cc_final: 0.7437 (tm-30) REVERT: B 58 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7494 (mttt) REVERT: C 57 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7335 (tm-30) REVERT: D 57 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7516 (tm-30) REVERT: D 83 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7928 (mt-10) REVERT: E 62 GLN cc_start: 0.7513 (mt0) cc_final: 0.7177 (mt0) REVERT: F 57 GLU cc_start: 0.8357 (tt0) cc_final: 0.7745 (tm-30) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1744 time to fit residues: 15.3953 Evaluate side-chains 84 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.179179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.139047 restraints weight = 2434.059| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.77 r_work: 0.4047 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2274 Z= 0.200 Angle : 0.557 5.868 3066 Z= 0.300 Chirality : 0.052 0.144 402 Planarity : 0.001 0.007 384 Dihedral : 5.105 14.871 324 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.70 % Allowed : 24.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.005 0.001 PHE A 94 *********************** 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 86 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.232 Fit side-chains REVERT: A 57 GLU cc_start: 0.8127 (tt0) cc_final: 0.7508 (tm-30) REVERT: A 58 LYS cc_start: 0.7991 (mmtp) cc_final: 0.7543 (mmmt) REVERT: A 60 LYS cc_start: 0.8498 (mptt) cc_final: 0.8288 (mptt) REVERT: B 57 GLU cc_start: 0.8049 (tt0) cc_final: 0.7453 (tm-30) REVERT: B 58 LYS cc_start: 0.8032 (mmtp) cc_final: 0.7526 (mttt) REVERT: C 45 LYS cc_start: 0.3419 (tptp) cc_final: 0.3163 (tptp) REVERT: C 57 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7341 (tm-30) REVERT: C 58 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8238 (mmtt) REVERT: D 57 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7622 (tm-30) REVERT: D 83 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7893 (mt-10) REVERT: E 62 GLN cc_start: 0.7280 (mt0) cc_final: 0.6939 (mt0) REVERT: F 57 GLU cc_start: 0.8341 (tt0) cc_final: 0.7631 (tm-30) outliers start: 13 outliers final: 12 residues processed: 78 average time/residue: 0.1695 time to fit residues: 15.0380 Evaluate side-chains 82 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain D 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 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: 0.0970 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- 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 = 0.178525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.138690 restraints weight = 2509.700| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 3.69 r_work: 0.4101 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2274 Z= 0.357 Angle : 0.639 5.873 3066 Z= 0.347 Chirality : 0.054 0.154 402 Planarity : 0.002 0.007 384 Dihedral : 5.620 16.592 324 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 6.14 % Allowed : 23.68 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.005 0.001 PHE D 94 ********************** 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 89 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.259 Fit side-chains REVERT: A 57 GLU cc_start: 0.8214 (tt0) cc_final: 0.7609 (tm-30) REVERT: A 58 LYS cc_start: 0.8188 (mmtp) cc_final: 0.7868 (mmtp) REVERT: C 57 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 98 ASP cc_start: 0.6891 (t0) cc_final: 0.6599 (t0) REVERT: D 57 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7799 (tm-30) REVERT: E 62 GLN cc_start: 0.7539 (mt0) cc_final: 0.7332 (mt0) REVERT: F 57 GLU cc_start: 0.8282 (tt0) cc_final: 0.8060 (tm-30) REVERT: F 58 LYS cc_start: 0.8319 (mmtp) cc_final: 0.7617 (mmmt) outliers start: 14 outliers final: 13 residues processed: 79 average time/residue: 0.1614 time to fit residues: 14.5574 Evaluate side-chains 87 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 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 3 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.175615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.135032 restraints weight = 2529.362| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 3.77 r_work: 0.4076 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2274 Z= 0.433 Angle : 0.737 7.896 3066 Z= 0.398 Chirality : 0.056 0.159 402 Planarity : 0.002 0.009 384 Dihedral : 5.903 17.201 324 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 7.89 % Allowed : 23.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.006 0.001 PHE D 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1540.31 seconds wall clock time: 28 minutes 22.01 seconds (1702.01 seconds total)