Starting phenix.real_space_refine on Fri May 9 15:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k23_61988/05_2025/9k23_61988.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k23_61988/05_2025/9k23_61988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k23_61988/05_2025/9k23_61988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k23_61988/05_2025/9k23_61988.map" model { file = "/net/cci-nas-00/data/ceres_data/9k23_61988/05_2025/9k23_61988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k23_61988/05_2025/9k23_61988.cif" } resolution = 2.6 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1728 2.51 5 N 480 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2772 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 462 Classifications: {'peptide': 66} Link IDs: {'TRANS': 65} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.14, per 1000 atoms: 0.77 Number of scatterers: 2772 At special positions: 0 Unit cell: (98.77, 128.65, 33.2, 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 564 8.00 N 480 7.00 C 1728 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: 0.61 Conformation dependent library (CDL) restraints added in 379.8 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 672 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 41 removed outlier: 6.579A pdb=" N GLY B 36 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N TYR A 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 38 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLY A 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 40 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 36 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N TYR C 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLY C 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 63 removed outlier: 6.402A pdb=" N GLN B 62 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN A 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 82 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 92 removed outlier: 6.647A pdb=" N PHE A 94 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 95 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS A 96 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 36 through 41 removed outlier: 6.579A pdb=" N GLY E 36 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N TYR D 39 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU E 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLY D 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL E 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY D 36 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N TYR F 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLY F 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 50 Processing sheet with id=AB1, first strand: chain 'E' and resid 61 through 63 removed outlier: 6.402A pdb=" N GLN E 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN D 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AB3, first strand: chain 'E' and resid 75 through 82 Processing sheet with id=AB4, first strand: chain 'E' and resid 88 through 96 removed outlier: 6.690A pdb=" N PHE E 94 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 95 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS E 96 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE D 94 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL F 95 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS D 96 " --> pdb=" O VAL F 95 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 222 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: 0.63 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 492 1.29 - 1.35: 426 1.35 - 1.41: 102 1.41 - 1.48: 456 1.48 - 1.54: 1308 Bond restraints: 2784 Sorted by residual: bond pdb=" N GLU A 46 " pdb=" CA GLU A 46 " ideal model delta sigma weight residual 1.461 1.452 0.009 1.20e-02 6.94e+03 5.70e-01 bond pdb=" CB GLN A 62 " pdb=" CG GLN A 62 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.56e-01 bond pdb=" CB GLN F 62 " pdb=" CG GLN F 62 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.34e-01 bond pdb=" CB GLN E 62 " pdb=" CG GLN E 62 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.18e-01 bond pdb=" CB GLN D 62 " pdb=" CG GLN D 62 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.15e-01 ... (remaining 2779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.58: 2873 0.58 - 1.15: 697 1.15 - 1.73: 138 1.73 - 2.30: 35 2.30 - 2.88: 19 Bond angle restraints: 3762 Sorted by residual: angle pdb=" CA GLY A 47 " pdb=" C GLY A 47 " pdb=" N VAL A 48 " ideal model delta sigma weight residual 114.98 116.78 -1.80 1.14e+00 7.69e-01 2.50e+00 angle pdb=" CA GLY C 47 " pdb=" C GLY C 47 " pdb=" N VAL C 48 " ideal model delta sigma weight residual 114.98 116.78 -1.80 1.14e+00 7.69e-01 2.48e+00 angle pdb=" CA GLY F 47 " pdb=" C GLY F 47 " pdb=" N VAL F 48 " ideal model delta sigma weight residual 114.98 116.77 -1.79 1.14e+00 7.69e-01 2.47e+00 angle pdb=" CA GLY E 47 " pdb=" C GLY E 47 " pdb=" N VAL E 48 " ideal model delta sigma weight residual 114.98 116.77 -1.79 1.14e+00 7.69e-01 2.46e+00 angle pdb=" CA GLY B 47 " pdb=" C GLY B 47 " pdb=" N VAL B 48 " ideal model delta sigma weight residual 114.98 116.76 -1.78 1.14e+00 7.69e-01 2.44e+00 ... (remaining 3757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 1506 16.17 - 32.34: 102 32.34 - 48.51: 18 48.51 - 64.68: 0 64.68 - 80.85: 6 Dihedral angle restraints: 1632 sinusoidal: 564 harmonic: 1068 Sorted by residual: dihedral pdb=" CA LYS E 34 " pdb=" C LYS E 34 " pdb=" N GLU E 35 " pdb=" CA GLU E 35 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA LYS D 34 " pdb=" C LYS D 34 " pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta harmonic sigma weight residual 180.00 164.18 15.82 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA LYS A 34 " pdb=" C LYS A 34 " pdb=" N GLU A 35 " pdb=" CA GLU A 35 " ideal model delta harmonic sigma weight residual 180.00 164.18 15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 1629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 236 0.025 - 0.050: 132 0.050 - 0.074: 40 0.074 - 0.099: 36 0.099 - 0.124: 48 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 66 " pdb=" N VAL A 66 " pdb=" C VAL A 66 " pdb=" CB VAL A 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA VAL F 66 " pdb=" N VAL F 66 " pdb=" C VAL F 66 " pdb=" CB VAL F 66 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA VAL B 66 " pdb=" N VAL B 66 " pdb=" C VAL B 66 " pdb=" CB VAL B 66 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 489 not shown) Planarity restraints: 468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 64 " 0.004 2.00e-02 2.50e+03 7.82e-03 6.12e-01 pdb=" C THR A 64 " -0.014 2.00e-02 2.50e+03 pdb=" O THR A 64 " 0.005 2.00e-02 2.50e+03 pdb=" N ASN A 65 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 64 " 0.004 2.00e-02 2.50e+03 7.75e-03 6.00e-01 pdb=" C THR F 64 " -0.013 2.00e-02 2.50e+03 pdb=" O THR F 64 " 0.005 2.00e-02 2.50e+03 pdb=" N ASN F 65 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 64 " 0.004 2.00e-02 2.50e+03 7.55e-03 5.70e-01 pdb=" C THR D 64 " -0.013 2.00e-02 2.50e+03 pdb=" O THR D 64 " 0.005 2.00e-02 2.50e+03 pdb=" N ASN D 65 " 0.004 2.00e-02 2.50e+03 ... (remaining 465 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 302 2.76 - 3.30: 2328 3.30 - 3.83: 4283 3.83 - 4.36: 4568 4.36 - 4.90: 9461 Nonbonded interactions: 20942 Sorted by model distance: nonbonded pdb=" O GLU F 83 " pdb=" ND2 ASN F 87 " model vdw 2.225 3.120 nonbonded pdb=" O GLU B 83 " pdb=" ND2 ASN B 87 " model vdw 2.225 3.120 nonbonded pdb=" O GLU D 83 " pdb=" ND2 ASN D 87 " model vdw 2.226 3.120 nonbonded pdb=" O GLU E 83 " pdb=" ND2 ASN E 87 " model vdw 2.226 3.120 nonbonded pdb=" O GLU C 83 " pdb=" ND2 ASN C 87 " model vdw 2.226 3.120 ... (remaining 20937 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: 0.03 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.060 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2784 Z= 0.253 Angle : 0.558 2.876 3762 Z= 0.339 Chirality : 0.050 0.124 492 Planarity : 0.002 0.008 468 Dihedral : 12.998 80.850 960 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.85 (0.31), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 PHE 0.013 0.004 PHE B 94 TYR 0.005 0.002 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.16609 ( 70) hydrogen bonds : angle 6.86336 ( 222) covalent geometry : bond 0.00522 ( 2784) covalent geometry : angle 0.55839 ( 3762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.317 Fit side-chains REVERT: B 34 LYS cc_start: 0.7586 (mttp) cc_final: 0.7309 (mmtt) REVERT: B 43 LYS cc_start: 0.8269 (tttm) cc_final: 0.7866 (ttmm) REVERT: A 35 GLU cc_start: 0.7313 (tt0) cc_final: 0.6762 (tm-30) REVERT: A 43 LYS cc_start: 0.8006 (tttm) cc_final: 0.7585 (ttmm) REVERT: A 98 ASP cc_start: 0.6901 (m-30) cc_final: 0.6556 (t0) REVERT: C 43 LYS cc_start: 0.8062 (tttm) cc_final: 0.7614 (ttmm) REVERT: E 43 LYS cc_start: 0.8342 (tttm) cc_final: 0.7886 (ttmt) REVERT: E 45 LYS cc_start: 0.8603 (tttt) cc_final: 0.8383 (tttt) REVERT: D 43 LYS cc_start: 0.8064 (tttm) cc_final: 0.7642 (ttmm) REVERT: F 43 LYS cc_start: 0.8060 (tttm) cc_final: 0.7594 (ttmm) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 1.4588 time to fit residues: 92.2799 Evaluate side-chains 44 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN A 65 ASN C 65 ASN E 65 ASN D 65 ASN F 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087033 restraints weight = 3556.518| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.56 r_work: 0.3382 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2784 Z= 0.212 Angle : 0.492 3.361 3762 Z= 0.282 Chirality : 0.050 0.128 492 Planarity : 0.002 0.009 468 Dihedral : 5.828 40.957 400 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.08 % Allowed : 12.15 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.24 (0.34), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.013 0.003 PHE A 94 TYR 0.006 0.002 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.02630 ( 70) hydrogen bonds : angle 3.96279 ( 222) covalent geometry : bond 0.00468 ( 2784) covalent geometry : angle 0.49192 ( 3762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.289 Fit side-chains REVERT: B 34 LYS cc_start: 0.7776 (mttp) cc_final: 0.7286 (mmtt) REVERT: B 43 LYS cc_start: 0.8553 (tttm) cc_final: 0.8090 (ttmm) REVERT: B 83 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7878 (tt0) REVERT: A 35 GLU cc_start: 0.7583 (tt0) cc_final: 0.7073 (tt0) REVERT: A 43 LYS cc_start: 0.8286 (tttm) cc_final: 0.7757 (ttmm) REVERT: A 98 ASP cc_start: 0.6959 (m-30) cc_final: 0.6528 (t0) REVERT: C 43 LYS cc_start: 0.8265 (tttm) cc_final: 0.7726 (ttmm) REVERT: C 87 ASN cc_start: 0.8677 (m-40) cc_final: 0.8454 (m110) REVERT: E 43 LYS cc_start: 0.8624 (tttm) cc_final: 0.8100 (ttmt) REVERT: E 45 LYS cc_start: 0.8657 (tttt) cc_final: 0.8289 (tmtt) REVERT: D 34 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7318 (tmmt) REVERT: D 43 LYS cc_start: 0.8307 (tttm) cc_final: 0.7783 (ttmm) REVERT: D 83 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8098 (tt0) REVERT: F 43 LYS cc_start: 0.8286 (tttm) cc_final: 0.7733 (ttmm) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 1.4558 time to fit residues: 96.4882 Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain D residue 98 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN A 79 GLN C 79 GLN C 87 ASN E 87 ASN D 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.105239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088080 restraints weight = 3571.132| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.56 r_work: 0.3406 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2784 Z= 0.213 Angle : 0.480 3.316 3762 Z= 0.274 Chirality : 0.050 0.137 492 Planarity : 0.002 0.009 468 Dihedral : 5.246 34.765 398 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.51 % Allowed : 12.50 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.04 (0.34), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.014 0.003 PHE B 94 TYR 0.006 0.002 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.02274 ( 70) hydrogen bonds : angle 3.68877 ( 222) covalent geometry : bond 0.00472 ( 2784) covalent geometry : angle 0.48009 ( 3762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.282 Fit side-chains REVERT: B 34 LYS cc_start: 0.7674 (mttp) cc_final: 0.7282 (mmtt) REVERT: B 43 LYS cc_start: 0.8555 (tttm) cc_final: 0.8084 (ttmm) REVERT: A 43 LYS cc_start: 0.8277 (tttm) cc_final: 0.7739 (ttmm) REVERT: C 43 LYS cc_start: 0.8229 (tttm) cc_final: 0.7712 (ttmm) REVERT: C 45 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8538 (tttt) REVERT: E 34 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7165 (mmtt) REVERT: E 43 LYS cc_start: 0.8582 (tttm) cc_final: 0.8050 (ttmt) REVERT: E 45 LYS cc_start: 0.8636 (tttt) cc_final: 0.8253 (tmtt) REVERT: D 34 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7311 (tmmt) REVERT: D 43 LYS cc_start: 0.8279 (tttm) cc_final: 0.7775 (ttmm) REVERT: D 83 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7992 (tt0) REVERT: F 43 LYS cc_start: 0.8266 (tttm) cc_final: 0.7691 (ttmm) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 1.4150 time to fit residues: 90.9334 Evaluate side-chains 64 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN E 87 ASN D 79 GLN D 87 ASN F 65 ASN F 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.103004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085549 restraints weight = 3691.366| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.57 r_work: 0.3360 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.048 2784 Z= 0.479 Angle : 0.707 4.491 3762 Z= 0.400 Chirality : 0.056 0.189 492 Planarity : 0.004 0.012 468 Dihedral : 6.309 41.236 398 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 5.56 % Allowed : 16.32 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.33 (0.33), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.018 0.004 PHE B 94 TYR 0.011 0.004 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 70) hydrogen bonds : angle 4.10824 ( 222) covalent geometry : bond 0.01067 ( 2784) covalent geometry : angle 0.70734 ( 3762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.327 Fit side-chains REVERT: B 34 LYS cc_start: 0.7824 (mttp) cc_final: 0.7319 (mmtt) REVERT: A 43 LYS cc_start: 0.8316 (tttm) cc_final: 0.7770 (ttmm) REVERT: C 43 LYS cc_start: 0.8253 (tttm) cc_final: 0.7738 (ttmm) REVERT: C 45 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8573 (tttt) REVERT: E 45 LYS cc_start: 0.8698 (tttt) cc_final: 0.8438 (tmtt) REVERT: D 34 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7326 (tmmt) REVERT: D 43 LYS cc_start: 0.8345 (tttm) cc_final: 0.7826 (ttmm) REVERT: D 83 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8083 (tt0) REVERT: F 34 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7933 (mtpp) REVERT: F 43 LYS cc_start: 0.8215 (tttm) cc_final: 0.7673 (ttmm) REVERT: F 83 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8050 (tt0) outliers start: 16 outliers final: 14 residues processed: 62 average time/residue: 1.3916 time to fit residues: 88.1631 Evaluate side-chains 66 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN E 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089510 restraints weight = 3529.723| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.55 r_work: 0.3424 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2784 Z= 0.137 Angle : 0.441 4.145 3762 Z= 0.253 Chirality : 0.050 0.127 492 Planarity : 0.002 0.010 468 Dihedral : 5.088 34.206 398 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.25 % Allowed : 17.71 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.96 (0.36), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.010 0.002 PHE B 94 TYR 0.005 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01756 ( 70) hydrogen bonds : angle 3.56899 ( 222) covalent geometry : bond 0.00291 ( 2784) covalent geometry : angle 0.44129 ( 3762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.297 Fit side-chains REVERT: B 34 LYS cc_start: 0.7735 (mttp) cc_final: 0.7240 (mmtt) REVERT: B 43 LYS cc_start: 0.8558 (tttm) cc_final: 0.8061 (ttmm) REVERT: A 43 LYS cc_start: 0.8276 (tttm) cc_final: 0.7744 (ttmm) REVERT: C 43 LYS cc_start: 0.8256 (tttm) cc_final: 0.7673 (ttmm) REVERT: C 45 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8514 (tttt) REVERT: E 34 LYS cc_start: 0.7655 (mttm) cc_final: 0.7067 (mmtt) REVERT: E 38 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8658 (tp) REVERT: E 43 LYS cc_start: 0.8543 (tttm) cc_final: 0.8082 (ttmt) REVERT: E 45 LYS cc_start: 0.8659 (tttt) cc_final: 0.8286 (tmtt) REVERT: D 34 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7250 (tmmt) REVERT: D 43 LYS cc_start: 0.8255 (tttm) cc_final: 0.7754 (ttmm) REVERT: F 43 LYS cc_start: 0.8209 (tttm) cc_final: 0.7666 (ttmm) outliers start: 18 outliers final: 9 residues processed: 72 average time/residue: 1.2517 time to fit residues: 92.1140 Evaluate side-chains 65 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN C 65 ASN C 87 ASN E 87 ASN D 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.086844 restraints weight = 3660.028| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.59 r_work: 0.3378 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2784 Z= 0.312 Angle : 0.571 3.899 3762 Z= 0.322 Chirality : 0.052 0.156 492 Planarity : 0.003 0.010 468 Dihedral : 5.062 17.119 396 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 6.25 % Allowed : 18.75 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.08 (0.35), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.014 0.004 PHE B 94 TYR 0.008 0.003 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02613 ( 70) hydrogen bonds : angle 3.88925 ( 222) covalent geometry : bond 0.00690 ( 2784) covalent geometry : angle 0.57082 ( 3762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.323 Fit side-chains REVERT: B 34 LYS cc_start: 0.7744 (mttp) cc_final: 0.7232 (mmtt) REVERT: B 43 LYS cc_start: 0.8585 (tttm) cc_final: 0.8047 (ttmm) REVERT: A 43 LYS cc_start: 0.8293 (tttm) cc_final: 0.7754 (ttmm) REVERT: C 43 LYS cc_start: 0.8227 (tttm) cc_final: 0.7702 (ttmm) REVERT: C 45 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8561 (tttt) REVERT: E 43 LYS cc_start: 0.8567 (tttm) cc_final: 0.8048 (ttmt) REVERT: D 34 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7488 (ttpp) REVERT: D 43 LYS cc_start: 0.8270 (tttm) cc_final: 0.7771 (ttmm) REVERT: F 43 LYS cc_start: 0.8259 (tttm) cc_final: 0.7703 (ttmm) outliers start: 18 outliers final: 14 residues processed: 59 average time/residue: 1.4961 time to fit residues: 90.0881 Evaluate side-chains 64 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.105136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.087812 restraints weight = 3655.969| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.61 r_work: 0.3391 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2784 Z= 0.240 Angle : 0.512 3.556 3762 Z= 0.291 Chirality : 0.051 0.131 492 Planarity : 0.002 0.009 468 Dihedral : 4.922 17.126 396 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.90 % Allowed : 19.44 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.00 (0.35), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.013 0.003 PHE B 94 TYR 0.007 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02260 ( 70) hydrogen bonds : angle 3.82992 ( 222) covalent geometry : bond 0.00525 ( 2784) covalent geometry : angle 0.51223 ( 3762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.349 Fit side-chains REVERT: B 34 LYS cc_start: 0.7707 (mttp) cc_final: 0.7225 (mmtt) REVERT: B 43 LYS cc_start: 0.8576 (tttm) cc_final: 0.8041 (ttmm) REVERT: A 43 LYS cc_start: 0.8288 (tttm) cc_final: 0.7738 (ttmm) REVERT: C 43 LYS cc_start: 0.8206 (tttm) cc_final: 0.7680 (ttmm) REVERT: C 45 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8540 (tttt) REVERT: E 43 LYS cc_start: 0.8549 (tttm) cc_final: 0.8048 (ttmt) REVERT: D 34 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7315 (tmmt) REVERT: D 43 LYS cc_start: 0.8235 (tttm) cc_final: 0.7742 (ttmm) REVERT: F 43 LYS cc_start: 0.8248 (tttm) cc_final: 0.7701 (ttmm) outliers start: 17 outliers final: 15 residues processed: 57 average time/residue: 1.6639 time to fit residues: 96.8041 Evaluate side-chains 63 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.106552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089322 restraints weight = 3594.326| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.59 r_work: 0.3416 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2784 Z= 0.169 Angle : 0.462 4.160 3762 Z= 0.262 Chirality : 0.050 0.125 492 Planarity : 0.002 0.011 468 Dihedral : 4.543 16.398 396 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.56 % Allowed : 19.79 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.83 (0.36), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.012 0.003 PHE B 94 TYR 0.005 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01849 ( 70) hydrogen bonds : angle 3.68810 ( 222) covalent geometry : bond 0.00365 ( 2784) covalent geometry : angle 0.46207 ( 3762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.288 Fit side-chains REVERT: B 34 LYS cc_start: 0.7684 (mttp) cc_final: 0.7240 (mmtt) REVERT: B 43 LYS cc_start: 0.8591 (tttm) cc_final: 0.8068 (ttmm) REVERT: A 43 LYS cc_start: 0.8290 (tttm) cc_final: 0.7752 (ttmm) REVERT: C 43 LYS cc_start: 0.8275 (tttm) cc_final: 0.7706 (ttmm) REVERT: C 45 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8546 (tttt) REVERT: E 34 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7385 (ttpp) REVERT: E 43 LYS cc_start: 0.8567 (tttm) cc_final: 0.8105 (ttmt) REVERT: D 34 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7269 (tmmt) REVERT: D 43 LYS cc_start: 0.8262 (tttm) cc_final: 0.7750 (ttmm) REVERT: F 34 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7694 (ttpt) REVERT: F 43 LYS cc_start: 0.8232 (tttm) cc_final: 0.7693 (ttmm) outliers start: 16 outliers final: 13 residues processed: 60 average time/residue: 1.4990 time to fit residues: 91.7895 Evaluate side-chains 66 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.106692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089485 restraints weight = 3594.446| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.59 r_work: 0.3417 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2784 Z= 0.165 Angle : 0.447 4.018 3762 Z= 0.255 Chirality : 0.050 0.124 492 Planarity : 0.002 0.011 468 Dihedral : 4.431 15.922 396 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.25 % Allowed : 19.10 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.75 (0.37), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.012 0.003 PHE B 94 TYR 0.005 0.002 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.01827 ( 70) hydrogen bonds : angle 3.65756 ( 222) covalent geometry : bond 0.00356 ( 2784) covalent geometry : angle 0.44659 ( 3762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.297 Fit side-chains REVERT: B 34 LYS cc_start: 0.7678 (mttp) cc_final: 0.7234 (mmtt) REVERT: B 43 LYS cc_start: 0.8564 (tttm) cc_final: 0.8061 (ttmm) REVERT: A 43 LYS cc_start: 0.8289 (tttm) cc_final: 0.7760 (ttmm) REVERT: C 43 LYS cc_start: 0.8266 (tttm) cc_final: 0.7718 (ttmm) REVERT: C 45 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8531 (tttt) REVERT: E 34 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7069 (mmtt) REVERT: E 38 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8629 (tp) REVERT: E 43 LYS cc_start: 0.8570 (tttm) cc_final: 0.8067 (ttmt) REVERT: D 34 LYS cc_start: 0.7852 (mtmm) cc_final: 0.7294 (tmmt) REVERT: D 43 LYS cc_start: 0.8274 (tttm) cc_final: 0.7768 (ttmm) REVERT: F 34 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7748 (ttpt) REVERT: F 43 LYS cc_start: 0.8260 (tttm) cc_final: 0.7705 (ttmm) outliers start: 18 outliers final: 12 residues processed: 57 average time/residue: 1.4097 time to fit residues: 82.0474 Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.107987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.090986 restraints weight = 3599.050| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.59 r_work: 0.3442 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2784 Z= 0.105 Angle : 0.400 3.785 3762 Z= 0.229 Chirality : 0.050 0.124 492 Planarity : 0.002 0.011 468 Dihedral : 4.031 14.730 396 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.82 % Allowed : 21.88 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.57 (0.38), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.009 0.002 PHE B 94 TYR 0.005 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.01500 ( 70) hydrogen bonds : angle 3.47571 ( 222) covalent geometry : bond 0.00220 ( 2784) covalent geometry : angle 0.40014 ( 3762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.319 Fit side-chains REVERT: B 34 LYS cc_start: 0.7723 (mttp) cc_final: 0.7296 (mmtt) REVERT: B 43 LYS cc_start: 0.8555 (tttm) cc_final: 0.8085 (ttmm) REVERT: A 43 LYS cc_start: 0.8297 (tttm) cc_final: 0.7780 (ttmm) REVERT: C 43 LYS cc_start: 0.8237 (tttm) cc_final: 0.7701 (ttmm) REVERT: C 45 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8486 (tttt) REVERT: E 34 LYS cc_start: 0.7600 (mtmm) cc_final: 0.7257 (ttpp) REVERT: E 43 LYS cc_start: 0.8608 (tttm) cc_final: 0.8106 (ttmt) REVERT: D 34 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7279 (tmmt) REVERT: D 43 LYS cc_start: 0.8265 (tttm) cc_final: 0.7777 (ttmm) REVERT: F 34 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7719 (ttpt) REVERT: F 43 LYS cc_start: 0.8230 (tttm) cc_final: 0.7712 (ttmm) outliers start: 11 outliers final: 9 residues processed: 54 average time/residue: 1.4875 time to fit residues: 81.9850 Evaluate side-chains 55 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086782 restraints weight = 3582.904| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.58 r_work: 0.3374 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.038 2784 Z= 0.368 Angle : 0.605 4.403 3762 Z= 0.343 Chirality : 0.053 0.141 492 Planarity : 0.003 0.011 468 Dihedral : 5.072 17.020 396 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.51 % Allowed : 21.53 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.94 (0.35), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.016 0.004 PHE B 94 TYR 0.009 0.004 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 70) hydrogen bonds : angle 4.02615 ( 222) covalent geometry : bond 0.00815 ( 2784) covalent geometry : angle 0.60538 ( 3762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.08 seconds wall clock time: 48 minutes 16.03 seconds (2896.03 seconds total)