Starting phenix.real_space_refine on Wed Sep 17 03:17:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k23_61988/09_2025/9k23_61988.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k23_61988/09_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_61988/09_2025/9k23_61988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k23_61988/09_2025/9k23_61988.map" model { file = "/net/cci-nas-00/data/ceres_data/9k23_61988/09_2025/9k23_61988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k23_61988/09_2025/9k23_61988.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2772 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" 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: A, C, E, D, F Time building chain proxies: 0.70, per 1000 atoms: 0.25 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: 0.22 Conformation dependent library (CDL) restraints added in 116.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.15 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: 0.36 Time building geometry restraints manager: 0.30 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.830 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.290 ------------------------------------------------------------------------------- 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 : 5.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.005 0.002 TYR C 39 PHE 0.013 0.004 PHE B 94 HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 2784) covalent geometry : angle 0.55839 ( 3762) hydrogen bonds : bond 0.16609 ( 70) hydrogen bonds : angle 6.86336 ( 222) *********************** 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 : 0.113 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: 0.6917 time to fit residues: 43.6440 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 : 0.114 ------------------------------------------------------------------------------- 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 24 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.104611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.087543 restraints weight = 3617.671| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.59 r_work: 0.3396 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1205 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= 0.170 Angle : 0.457 3.270 3762 Z= 0.263 Chirality : 0.050 0.125 492 Planarity : 0.002 0.008 468 Dihedral : 5.593 38.779 400 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.39 % Allowed : 12.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.34), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.013 0.003 PHE A 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 2784) covalent geometry : angle 0.45655 ( 3762) hydrogen bonds : bond 0.02247 ( 70) hydrogen bonds : angle 3.89519 ( 222) *********************** 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: 4 poor density : 65 time to evaluate : 0.147 Fit side-chains REVERT: B 34 LYS cc_start: 0.7686 (mttp) cc_final: 0.7234 (mmtt) REVERT: B 43 LYS cc_start: 0.8561 (tttm) cc_final: 0.8101 (ttmm) REVERT: B 83 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7879 (tt0) REVERT: A 35 GLU cc_start: 0.7598 (tt0) cc_final: 0.7085 (tt0) REVERT: A 43 LYS cc_start: 0.8265 (tttm) cc_final: 0.7742 (ttmm) REVERT: A 98 ASP cc_start: 0.6907 (m-30) cc_final: 0.6476 (t0) REVERT: C 43 LYS cc_start: 0.8270 (tttm) cc_final: 0.7731 (ttmm) REVERT: C 87 ASN cc_start: 0.8646 (m-40) cc_final: 0.8421 (m110) REVERT: E 34 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7157 (mmtt) REVERT: E 43 LYS cc_start: 0.8617 (tttm) cc_final: 0.8106 (ttmt) REVERT: E 45 LYS cc_start: 0.8649 (tttt) cc_final: 0.8316 (tmtt) REVERT: D 34 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7291 (tmmt) REVERT: D 43 LYS cc_start: 0.8291 (tttm) cc_final: 0.7771 (ttmm) REVERT: D 83 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8006 (mt-10) REVERT: F 43 LYS cc_start: 0.8270 (tttm) cc_final: 0.7705 (ttmm) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.6990 time to fit residues: 47.7592 Evaluate side-chains 60 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 ASP 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 18 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN E 79 GLN E 87 ASN D 79 GLN D 87 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 = 0.3739 r_free = 0.3739 target = 0.105631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.088513 restraints weight = 3638.467| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.59 r_work: 0.3414 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2784 Z= 0.172 Angle : 0.446 3.889 3762 Z= 0.254 Chirality : 0.050 0.128 492 Planarity : 0.002 0.010 468 Dihedral : 4.964 33.506 398 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.82 % Allowed : 12.50 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.91 (0.35), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR A 39 PHE 0.013 0.003 PHE B 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2784) covalent geometry : angle 0.44647 ( 3762) hydrogen bonds : bond 0.02031 ( 70) hydrogen bonds : angle 3.56490 ( 222) *********************** 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 72 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.120 Fit side-chains REVERT: B 34 LYS cc_start: 0.7585 (mttp) cc_final: 0.7234 (mmtt) REVERT: B 43 LYS cc_start: 0.8563 (tttm) cc_final: 0.8104 (ttmm) REVERT: A 43 LYS cc_start: 0.8268 (tttm) cc_final: 0.7744 (ttmm) REVERT: C 43 LYS cc_start: 0.8235 (tttm) cc_final: 0.7732 (ttmm) REVERT: C 45 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8535 (tttt) REVERT: E 34 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7197 (mmtt) REVERT: E 38 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8677 (tp) REVERT: E 43 LYS cc_start: 0.8613 (tttm) cc_final: 0.8103 (ttmt) REVERT: E 45 LYS cc_start: 0.8635 (tttt) cc_final: 0.8317 (tmtt) REVERT: D 34 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7443 (ttpp) REVERT: D 43 LYS cc_start: 0.8297 (tttm) cc_final: 0.7789 (ttmm) REVERT: F 43 LYS cc_start: 0.8270 (tttm) cc_final: 0.7710 (ttmm) outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 0.7694 time to fit residues: 50.1156 Evaluate side-chains 64 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.067 ------------------------------------------------------------------------------- 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 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 59 THR Chi-restraints excluded: chain D residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN D 87 ASN F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.107040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.090259 restraints weight = 3565.437| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.55 r_work: 0.3440 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2784 Z= 0.116 Angle : 0.397 4.824 3762 Z= 0.227 Chirality : 0.049 0.125 492 Planarity : 0.002 0.010 468 Dihedral : 4.611 30.731 398 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.82 % Allowed : 15.62 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.37), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.011 0.003 PHE A 94 HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2784) covalent geometry : angle 0.39743 ( 3762) hydrogen bonds : bond 0.01578 ( 70) hydrogen bonds : angle 3.34491 ( 222) *********************** 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 73 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.119 Fit side-chains REVERT: B 34 LYS cc_start: 0.7744 (mttp) cc_final: 0.7274 (mmtt) REVERT: B 43 LYS cc_start: 0.8539 (tttm) cc_final: 0.8084 (ttmm) REVERT: A 43 LYS cc_start: 0.8257 (tttm) cc_final: 0.7752 (ttmm) REVERT: C 43 LYS cc_start: 0.8290 (tttm) cc_final: 0.7764 (ttmm) REVERT: E 34 LYS cc_start: 0.7589 (mtmm) cc_final: 0.7071 (mmtt) REVERT: E 43 LYS cc_start: 0.8605 (tttm) cc_final: 0.8091 (ttmt) REVERT: E 45 LYS cc_start: 0.8619 (tttt) cc_final: 0.8355 (tmtt) REVERT: D 34 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7310 (tmmt) REVERT: D 43 LYS cc_start: 0.8321 (tttm) cc_final: 0.7826 (ttmm) REVERT: F 43 LYS cc_start: 0.8262 (tttm) cc_final: 0.7730 (ttmm) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 0.7481 time to fit residues: 49.5468 Evaluate side-chains 60 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 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 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 14 optimal weight: 0.0170 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN C 79 GLN 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 = 0.3773 r_free = 0.3773 target = 0.108216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091506 restraints weight = 3506.094| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.55 r_work: 0.3452 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.002 0.011 2784 Z= 0.091 Angle : 0.380 4.049 3762 Z= 0.216 Chirality : 0.050 0.124 492 Planarity : 0.001 0.011 468 Dihedral : 3.805 13.427 396 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.82 % Allowed : 17.71 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.38), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.010 0.002 PHE A 94 HIS 0.001 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 2784) covalent geometry : angle 0.37984 ( 3762) hydrogen bonds : bond 0.01428 ( 70) hydrogen bonds : angle 3.22003 ( 222) *********************** 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 68 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.104 Fit side-chains REVERT: B 34 LYS cc_start: 0.7699 (mttp) cc_final: 0.7237 (mmtt) REVERT: B 43 LYS cc_start: 0.8543 (tttm) cc_final: 0.8064 (ttmm) REVERT: A 43 LYS cc_start: 0.8296 (tttm) cc_final: 0.7782 (ttmm) REVERT: C 43 LYS cc_start: 0.8311 (tttm) cc_final: 0.7812 (ttmm) REVERT: C 45 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8462 (tttt) REVERT: E 34 LYS cc_start: 0.7635 (mtmm) cc_final: 0.7397 (ttpt) REVERT: E 43 LYS cc_start: 0.8635 (tttm) cc_final: 0.8107 (ttmm) REVERT: E 45 LYS cc_start: 0.8611 (tttt) cc_final: 0.8394 (tmtt) REVERT: D 34 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7223 (tmmt) REVERT: D 43 LYS cc_start: 0.8346 (tttm) cc_final: 0.7800 (ttmm) REVERT: F 34 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7359 (mptp) REVERT: F 43 LYS cc_start: 0.8221 (tttm) cc_final: 0.7704 (ttmm) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.7623 time to fit residues: 47.3655 Evaluate side-chains 59 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 45 LYS 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 D residue 98 ASP Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN D 87 ASN F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.105349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088022 restraints weight = 3617.842| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.58 r_work: 0.3395 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2784 Z= 0.268 Angle : 0.517 3.716 3762 Z= 0.292 Chirality : 0.050 0.131 492 Planarity : 0.003 0.009 468 Dihedral : 4.604 15.985 396 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.56 % Allowed : 18.06 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.36), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.003 TYR A 39 PHE 0.017 0.004 PHE B 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 2784) covalent geometry : angle 0.51650 ( 3762) hydrogen bonds : bond 0.02253 ( 70) hydrogen bonds : angle 3.65397 ( 222) *********************** 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 73 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.111 Fit side-chains REVERT: B 34 LYS cc_start: 0.7717 (mttp) cc_final: 0.7229 (mmtt) REVERT: B 43 LYS cc_start: 0.8526 (tttm) cc_final: 0.8037 (ttmm) REVERT: A 43 LYS cc_start: 0.8292 (tttm) cc_final: 0.7772 (ttmm) REVERT: C 43 LYS cc_start: 0.8269 (tttm) cc_final: 0.7733 (ttmm) REVERT: C 45 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8531 (tttt) REVERT: E 43 LYS cc_start: 0.8591 (tttm) cc_final: 0.8067 (ttmt) REVERT: D 34 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7296 (tmmt) REVERT: D 43 LYS cc_start: 0.8312 (tttm) cc_final: 0.7792 (ttmm) REVERT: F 43 LYS cc_start: 0.8249 (tttm) cc_final: 0.7665 (ttmm) outliers start: 16 outliers final: 7 residues processed: 61 average time/residue: 0.7354 time to fit residues: 45.6737 Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 C residue 45 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.106870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.089967 restraints weight = 3547.823| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.57 r_work: 0.3434 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2784 Z= 0.145 Angle : 0.438 4.978 3762 Z= 0.245 Chirality : 0.050 0.124 492 Planarity : 0.002 0.011 468 Dihedral : 4.222 15.245 396 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.47 % Allowed : 20.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.37), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR A 39 PHE 0.012 0.003 PHE B 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 2784) covalent geometry : angle 0.43822 ( 3762) hydrogen bonds : bond 0.01729 ( 70) hydrogen bonds : angle 3.46102 ( 222) *********************** 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 67 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.147 Fit side-chains REVERT: B 34 LYS cc_start: 0.7636 (mttp) cc_final: 0.7153 (mmtt) REVERT: B 43 LYS cc_start: 0.8556 (tttm) cc_final: 0.8076 (ttmm) REVERT: A 43 LYS cc_start: 0.8272 (tttm) cc_final: 0.7771 (ttmm) REVERT: C 43 LYS cc_start: 0.8258 (tttm) cc_final: 0.7734 (ttmm) REVERT: C 45 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8506 (tttt) REVERT: E 34 LYS cc_start: 0.7671 (mtmm) cc_final: 0.7401 (ttpt) REVERT: E 43 LYS cc_start: 0.8568 (tttm) cc_final: 0.8069 (ttmt) REVERT: D 34 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7091 (tmmt) REVERT: D 43 LYS cc_start: 0.8298 (tttm) cc_final: 0.7800 (ttmm) REVERT: F 34 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7318 (mptp) REVERT: F 43 LYS cc_start: 0.8264 (tttm) cc_final: 0.7724 (ttmm) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.6932 time to fit residues: 41.7112 Evaluate side-chains 60 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 45 LYS 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 D residue 98 ASP Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN D 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.104987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.087704 restraints weight = 3650.533| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.59 r_work: 0.3389 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 2784 Z= 0.301 Angle : 0.559 3.995 3762 Z= 0.314 Chirality : 0.051 0.142 492 Planarity : 0.003 0.009 468 Dihedral : 4.866 16.186 396 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.21 % Allowed : 19.10 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.35), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.003 TYR C 39 PHE 0.017 0.004 PHE B 94 HIS 0.003 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 2784) covalent geometry : angle 0.55873 ( 3762) hydrogen bonds : bond 0.02520 ( 70) hydrogen bonds : angle 3.79014 ( 222) *********************** 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 68 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.103 Fit side-chains REVERT: B 34 LYS cc_start: 0.7646 (mttp) cc_final: 0.7201 (mmtt) REVERT: B 43 LYS cc_start: 0.8578 (tttm) cc_final: 0.8044 (ttmm) REVERT: A 43 LYS cc_start: 0.8301 (tttm) cc_final: 0.7763 (ttmm) REVERT: C 43 LYS cc_start: 0.8223 (tttm) cc_final: 0.7730 (ttmm) REVERT: C 45 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8519 (tttt) REVERT: E 34 LYS cc_start: 0.7841 (mtmm) cc_final: 0.7262 (mmtt) REVERT: E 38 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8624 (tp) REVERT: E 43 LYS cc_start: 0.8578 (tttm) cc_final: 0.8096 (ttmt) REVERT: D 34 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7304 (tmmt) REVERT: D 43 LYS cc_start: 0.8266 (tttm) cc_final: 0.7804 (ttmm) REVERT: F 43 LYS cc_start: 0.8218 (tttm) cc_final: 0.7659 (ttmm) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.7275 time to fit residues: 41.4840 Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.108311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091452 restraints weight = 3651.582| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.59 r_work: 0.3450 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2784 Z= 0.096 Angle : 0.413 5.032 3762 Z= 0.232 Chirality : 0.050 0.126 492 Planarity : 0.002 0.012 468 Dihedral : 4.085 15.037 396 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.78 % Allowed : 22.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.37), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.009 0.002 PHE D 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 2784) covalent geometry : angle 0.41338 ( 3762) hydrogen bonds : bond 0.01494 ( 70) hydrogen bonds : angle 3.38843 ( 222) *********************** 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 67 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.125 Fit side-chains REVERT: B 43 LYS cc_start: 0.8529 (tttm) cc_final: 0.8067 (ttmm) REVERT: A 43 LYS cc_start: 0.8260 (tttm) cc_final: 0.7767 (ttmm) REVERT: C 43 LYS cc_start: 0.8250 (tttm) cc_final: 0.7729 (ttmm) REVERT: C 45 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8463 (tttt) REVERT: E 34 LYS cc_start: 0.7633 (mtmm) cc_final: 0.7403 (ttpt) REVERT: E 43 LYS cc_start: 0.8573 (tttm) cc_final: 0.8066 (ttmt) REVERT: D 34 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7257 (tmmt) REVERT: D 43 LYS cc_start: 0.8314 (tttm) cc_final: 0.7818 (ttmm) REVERT: F 43 LYS cc_start: 0.8228 (tttm) cc_final: 0.7704 (ttmm) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.6432 time to fit residues: 40.6433 Evaluate side-chains 60 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 45 LYS 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 D residue 98 ASP Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.110285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093824 restraints weight = 3617.815| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.58 r_work: 0.3490 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 2784 Z= 0.076 Angle : 0.401 5.162 3762 Z= 0.222 Chirality : 0.050 0.125 492 Planarity : 0.001 0.012 468 Dihedral : 3.644 12.923 396 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.74 % Allowed : 23.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.38), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.001 TYR D 39 PHE 0.008 0.002 PHE A 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00149 ( 2784) covalent geometry : angle 0.40066 ( 3762) hydrogen bonds : bond 0.01304 ( 70) hydrogen bonds : angle 3.21783 ( 222) ********************** 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 56 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.112 Fit side-chains REVERT: B 43 LYS cc_start: 0.8543 (tttm) cc_final: 0.8059 (ttmm) REVERT: A 43 LYS cc_start: 0.8348 (tttm) cc_final: 0.7800 (ttmm) REVERT: C 43 LYS cc_start: 0.8275 (tttm) cc_final: 0.7783 (ttmm) REVERT: C 45 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8379 (tttt) REVERT: E 34 LYS cc_start: 0.7604 (mtmm) cc_final: 0.6991 (mptp) REVERT: E 43 LYS cc_start: 0.8600 (tttm) cc_final: 0.8087 (ttmt) REVERT: D 34 LYS cc_start: 0.7506 (mtmm) cc_final: 0.7080 (tmmt) REVERT: D 43 LYS cc_start: 0.8368 (tttm) cc_final: 0.7783 (ttmm) REVERT: F 34 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7831 (ttpt) REVERT: F 43 LYS cc_start: 0.8252 (tttm) cc_final: 0.7696 (ttmm) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.7844 time to fit residues: 41.5384 Evaluate side-chains 54 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain D residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.106729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089829 restraints weight = 3532.973| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.56 r_work: 0.3422 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2784 Z= 0.186 Angle : 0.479 4.565 3762 Z= 0.267 Chirality : 0.050 0.122 492 Planarity : 0.002 0.012 468 Dihedral : 4.229 14.657 396 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.12 % Allowed : 22.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.37), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.003 TYR D 39 PHE 0.014 0.003 PHE B 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 2784) covalent geometry : angle 0.47881 ( 3762) hydrogen bonds : bond 0.01850 ( 70) hydrogen bonds : angle 3.51223 ( 222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1444.42 seconds wall clock time: 25 minutes 21.49 seconds (1521.49 seconds total)