Starting phenix.real_space_refine on Sat Apr 26 17:32:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k23_61988/04_2025/9k23_61988.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k23_61988/04_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_61988/04_2025/9k23_61988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k23_61988/04_2025/9k23_61988.map" model { file = "/net/cci-nas-00/data/ceres_data/9k23_61988/04_2025/9k23_61988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k23_61988/04_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-5669/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: 2.57, per 1000 atoms: 0.93 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: 0.67 Conformation dependent library (CDL) restraints added in 400.7 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: 0.46 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: 0.67 Time building geometry restraints manager: 0.81 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: 2.300 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: 12.700 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- 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 : 0.284 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: 1.4557 time to fit residues: 92.0987 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 : 0.296 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087032 restraints weight = 3556.528| |-----------------------------------------------------------------------------| 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 3.96278 ( 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 : 0.323 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: 0.8089 (ttmm) REVERT: B 83 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7878 (tt0) REVERT: A 35 GLU cc_start: 0.7581 (tt0) cc_final: 0.7070 (tt0) REVERT: A 43 LYS cc_start: 0.8285 (tttm) cc_final: 0.7755 (ttmm) REVERT: A 98 ASP cc_start: 0.6958 (m-30) cc_final: 0.6526 (t0) REVERT: C 43 LYS cc_start: 0.8264 (tttm) cc_final: 0.7724 (ttmm) REVERT: C 87 ASN cc_start: 0.8678 (m-40) cc_final: 0.8454 (m110) REVERT: E 43 LYS cc_start: 0.8624 (tttm) cc_final: 0.8099 (ttmt) REVERT: E 45 LYS cc_start: 0.8659 (tttt) cc_final: 0.8290 (tmtt) REVERT: D 34 LYS cc_start: 0.7952 (mtmm) cc_final: 0.7317 (tmmt) REVERT: D 43 LYS cc_start: 0.8307 (tttm) cc_final: 0.7782 (ttmm) REVERT: D 83 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8099 (tt0) REVERT: F 43 LYS cc_start: 0.8284 (tttm) cc_final: 0.7730 (ttmm) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 1.5250 time to fit residues: 101.0291 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 : 0.288 ------------------------------------------------------------------------------- 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: 0.0060 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 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: 1.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN E 87 ASN D 87 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 = 0.106729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.089714 restraints weight = 3528.155| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.56 r_work: 0.3433 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1508 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= 0.119 Angle : 0.410 4.148 3762 Z= 0.233 Chirality : 0.050 0.125 492 Planarity : 0.002 0.009 468 Dihedral : 4.738 31.722 398 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.74 % Allowed : 13.89 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.86 (0.36), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.011 0.003 PHE A 94 TYR 0.005 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.01772 ( 70) hydrogen bonds : angle 3.48081 ( 222) covalent geometry : bond 0.00257 ( 2784) covalent geometry : angle 0.40993 ( 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 69 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.315 Fit side-chains REVERT: B 34 LYS cc_start: 0.7595 (mttp) cc_final: 0.7235 (mmtt) REVERT: B 43 LYS cc_start: 0.8552 (tttm) cc_final: 0.8090 (ttmm) REVERT: B 83 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7897 (tt0) REVERT: A 43 LYS cc_start: 0.8253 (tttm) cc_final: 0.7728 (ttmm) REVERT: C 43 LYS cc_start: 0.8227 (tttm) cc_final: 0.7720 (ttmm) REVERT: C 87 ASN cc_start: 0.8532 (m-40) cc_final: 0.8274 (m110) REVERT: E 34 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7064 (mmtt) REVERT: E 38 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8631 (tp) REVERT: E 43 LYS cc_start: 0.8601 (tttm) cc_final: 0.8082 (ttmt) REVERT: E 45 LYS cc_start: 0.8629 (tttt) cc_final: 0.8342 (tmtt) REVERT: D 34 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7415 (ttpp) REVERT: D 43 LYS cc_start: 0.8275 (tttm) cc_final: 0.7759 (ttmm) REVERT: F 43 LYS cc_start: 0.8244 (tttm) cc_final: 0.7697 (ttmm) outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 1.4496 time to fit residues: 96.0843 Evaluate side-chains 61 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.0980 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3745 r_free = 0.3745 target = 0.105974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.088812 restraints weight = 3569.250| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.55 r_work: 0.3422 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2784 Z= 0.177 Angle : 0.444 3.593 3762 Z= 0.254 Chirality : 0.050 0.125 492 Planarity : 0.002 0.011 468 Dihedral : 4.357 14.977 396 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.51 % Allowed : 15.28 % Favored : 80.21 % 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: -2.73 (0.36), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.28), 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 E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01939 ( 70) hydrogen bonds : angle 3.49758 ( 222) covalent geometry : bond 0.00387 ( 2784) covalent geometry : angle 0.44415 ( 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: 13 poor density : 58 time to evaluate : 0.287 Fit side-chains REVERT: B 34 LYS cc_start: 0.7576 (mttp) cc_final: 0.7219 (mmtt) REVERT: B 43 LYS cc_start: 0.8549 (tttm) cc_final: 0.8091 (ttmm) REVERT: A 43 LYS cc_start: 0.8274 (tttm) cc_final: 0.7758 (ttmm) REVERT: C 43 LYS cc_start: 0.8276 (tttm) cc_final: 0.7738 (ttmm) REVERT: C 45 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8531 (tttt) REVERT: E 34 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7213 (mmtt) REVERT: E 43 LYS cc_start: 0.8599 (tttm) cc_final: 0.8089 (ttmt) REVERT: E 45 LYS cc_start: 0.8634 (tttt) cc_final: 0.8290 (tmtt) REVERT: D 34 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7544 (ttpp) REVERT: D 43 LYS cc_start: 0.8297 (tttm) cc_final: 0.7792 (ttmm) REVERT: F 43 LYS cc_start: 0.8236 (tttm) cc_final: 0.7693 (ttmm) outliers start: 13 outliers final: 7 residues processed: 62 average time/residue: 1.5154 time to fit residues: 95.8394 Evaluate side-chains 61 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.0570 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 overall best weight: 2.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN A 79 GLN C 79 GLN E 87 ASN F 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089204 restraints weight = 3510.782| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.53 r_work: 0.3415 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1845 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= 0.168 Angle : 0.439 3.848 3762 Z= 0.250 Chirality : 0.050 0.122 492 Planarity : 0.002 0.010 468 Dihedral : 4.322 14.693 396 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -2.69 (0.37), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.013 0.003 PHE B 94 TYR 0.006 0.002 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.01845 ( 70) hydrogen bonds : angle 3.47008 ( 222) covalent geometry : bond 0.00367 ( 2784) covalent geometry : angle 0.43870 ( 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 73 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.287 Fit side-chains REVERT: B 34 LYS cc_start: 0.7679 (mttp) cc_final: 0.7248 (mmtt) REVERT: B 43 LYS cc_start: 0.8544 (tttm) cc_final: 0.8082 (ttmm) REVERT: A 43 LYS cc_start: 0.8275 (tttm) cc_final: 0.7761 (ttmm) REVERT: C 43 LYS cc_start: 0.8261 (tttm) cc_final: 0.7722 (ttmm) REVERT: C 45 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8515 (tttt) REVERT: E 34 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7137 (mmtt) REVERT: E 38 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8625 (tp) REVERT: E 43 LYS cc_start: 0.8595 (tttm) cc_final: 0.8081 (ttmt) REVERT: E 45 LYS cc_start: 0.8623 (tttt) cc_final: 0.8294 (tmtt) REVERT: D 34 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7340 (tmmt) REVERT: D 43 LYS cc_start: 0.8309 (tttm) cc_final: 0.7799 (ttmm) REVERT: F 43 LYS cc_start: 0.8228 (tttm) cc_final: 0.7684 (ttmm) outliers start: 16 outliers final: 9 residues processed: 60 average time/residue: 1.4947 time to fit residues: 91.4467 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 : 0.333 ------------------------------------------------------------------------------- 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 C residue 45 LYS Chi-restraints excluded: chain E residue 38 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN E 87 ASN D 79 GLN D 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.087920 restraints weight = 3632.783| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.58 r_work: 0.3407 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1881 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= 0.198 Angle : 0.469 3.989 3762 Z= 0.265 Chirality : 0.050 0.125 492 Planarity : 0.002 0.011 468 Dihedral : 4.438 15.058 396 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.86 % Allowed : 18.06 % Favored : 77.08 % 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: -2.73 (0.36), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.014 0.003 PHE B 94 TYR 0.007 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01986 ( 70) hydrogen bonds : angle 3.57501 ( 222) covalent geometry : bond 0.00436 ( 2784) covalent geometry : angle 0.46893 ( 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: 14 poor density : 56 time to evaluate : 0.308 Fit side-chains REVERT: B 34 LYS cc_start: 0.7731 (mttp) cc_final: 0.7250 (mmtt) REVERT: B 43 LYS cc_start: 0.8557 (tttm) cc_final: 0.8085 (ttmm) REVERT: A 43 LYS cc_start: 0.8284 (tttm) cc_final: 0.7765 (ttmm) REVERT: C 43 LYS cc_start: 0.8243 (tttm) cc_final: 0.7713 (ttmm) REVERT: C 45 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8525 (tttt) REVERT: E 34 LYS cc_start: 0.7701 (mttm) cc_final: 0.7158 (mmtt) REVERT: E 43 LYS cc_start: 0.8564 (tttm) cc_final: 0.8041 (ttmt) REVERT: E 45 LYS cc_start: 0.8639 (tttt) cc_final: 0.8266 (tmtt) REVERT: D 34 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7384 (tmmt) REVERT: D 43 LYS cc_start: 0.8296 (tttm) cc_final: 0.7780 (ttmm) REVERT: F 43 LYS cc_start: 0.8274 (tttm) cc_final: 0.7702 (ttmm) outliers start: 14 outliers final: 10 residues processed: 60 average time/residue: 1.4582 time to fit residues: 89.3910 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 : 0.377 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.105506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088086 restraints weight = 3646.573| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.59 r_work: 0.3397 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: 0.8544 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 2784 Z= 0.260 Angle : 0.522 4.081 3762 Z= 0.295 Chirality : 0.051 0.141 492 Planarity : 0.002 0.010 468 Dihedral : 4.735 15.838 396 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.86 % Allowed : 18.40 % Favored : 76.74 % 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: -2.89 (0.36), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.015 0.004 PHE B 94 TYR 0.008 0.003 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02335 ( 70) hydrogen bonds : angle 3.75920 ( 222) covalent geometry : bond 0.00576 ( 2784) covalent geometry : angle 0.52186 ( 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: 14 poor density : 54 time to evaluate : 0.301 Fit side-chains REVERT: B 34 LYS cc_start: 0.7663 (mttp) cc_final: 0.7235 (mmtt) REVERT: B 43 LYS cc_start: 0.8575 (tttm) cc_final: 0.8088 (ttmm) REVERT: A 43 LYS cc_start: 0.8299 (tttm) cc_final: 0.7767 (ttmm) REVERT: C 34 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7867 (ttpt) REVERT: C 43 LYS cc_start: 0.8211 (tttm) cc_final: 0.7716 (ttmm) REVERT: C 45 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8552 (tttt) REVERT: E 34 LYS cc_start: 0.7640 (mttm) cc_final: 0.7177 (mmtt) REVERT: E 43 LYS cc_start: 0.8545 (tttm) cc_final: 0.8085 (ttmt) REVERT: D 34 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7314 (tmmt) REVERT: D 43 LYS cc_start: 0.8282 (tttm) cc_final: 0.7789 (ttmm) REVERT: F 43 LYS cc_start: 0.8235 (tttm) cc_final: 0.7682 (ttmm) outliers start: 14 outliers final: 11 residues processed: 56 average time/residue: 1.6052 time to fit residues: 91.6213 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 : 0.323 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088158 restraints weight = 3611.251| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.59 r_work: 0.3395 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2784 Z= 0.260 Angle : 0.521 3.758 3762 Z= 0.296 Chirality : 0.051 0.135 492 Planarity : 0.002 0.010 468 Dihedral : 4.794 15.895 396 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.51 % Allowed : 19.44 % 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: -2.98 (0.35), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.015 0.004 PHE B 94 TYR 0.008 0.003 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02339 ( 70) hydrogen bonds : angle 3.80946 ( 222) covalent geometry : bond 0.00572 ( 2784) covalent geometry : angle 0.52146 ( 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 67 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.331 Fit side-chains REVERT: B 34 LYS cc_start: 0.7634 (mttp) cc_final: 0.7208 (mmtt) REVERT: B 43 LYS cc_start: 0.8580 (tttm) cc_final: 0.8058 (ttmm) REVERT: A 43 LYS cc_start: 0.8300 (tttm) cc_final: 0.7763 (ttmm) REVERT: C 34 LYS cc_start: 0.8353 (ttpp) cc_final: 0.7926 (ttpt) REVERT: C 43 LYS cc_start: 0.8213 (tttm) cc_final: 0.7715 (ttmm) REVERT: C 45 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8549 (tttt) REVERT: E 34 LYS cc_start: 0.7655 (mttm) cc_final: 0.7116 (mmtt) REVERT: E 43 LYS cc_start: 0.8536 (tttm) cc_final: 0.8050 (ttmt) REVERT: D 34 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7287 (tmmt) REVERT: D 43 LYS cc_start: 0.8293 (tttm) cc_final: 0.7790 (ttmm) REVERT: F 43 LYS cc_start: 0.8237 (tttm) cc_final: 0.7685 (ttmm) outliers start: 13 outliers final: 11 residues processed: 56 average time/residue: 1.5603 time to fit residues: 89.0533 Evaluate side-chains 63 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.0270 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.107094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089946 restraints weight = 3588.165| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.58 r_work: 0.3431 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1995 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= 0.144 Angle : 0.440 4.229 3762 Z= 0.249 Chirality : 0.050 0.124 492 Planarity : 0.002 0.012 468 Dihedral : 4.312 15.219 396 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.82 % Allowed : 20.14 % 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: -2.75 (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 F 50 PHE 0.011 0.003 PHE B 94 TYR 0.006 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01717 ( 70) hydrogen bonds : angle 3.58545 ( 222) covalent geometry : bond 0.00307 ( 2784) covalent geometry : angle 0.44031 ( 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 66 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.324 Fit side-chains REVERT: B 34 LYS cc_start: 0.7566 (mttp) cc_final: 0.7092 (mmtt) REVERT: B 43 LYS cc_start: 0.8538 (tttm) cc_final: 0.8068 (ttmm) REVERT: A 43 LYS cc_start: 0.8293 (tttm) cc_final: 0.7779 (ttmm) REVERT: C 43 LYS cc_start: 0.8250 (tttm) cc_final: 0.7721 (ttmm) REVERT: C 45 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8526 (tttt) REVERT: E 34 LYS cc_start: 0.7747 (mttm) cc_final: 0.7195 (mmtt) REVERT: E 43 LYS cc_start: 0.8544 (tttm) cc_final: 0.8015 (ttmm) REVERT: D 34 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7290 (tmmt) REVERT: D 43 LYS cc_start: 0.8280 (tttm) cc_final: 0.7780 (ttmm) REVERT: F 43 LYS cc_start: 0.8250 (tttm) cc_final: 0.7716 (ttmm) outliers start: 11 outliers final: 7 residues processed: 58 average time/residue: 1.5271 time to fit residues: 90.3624 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 : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 45 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.107240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090076 restraints weight = 3605.569| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.58 r_work: 0.3431 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2026 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= 0.150 Angle : 0.433 4.181 3762 Z= 0.247 Chirality : 0.049 0.123 492 Planarity : 0.002 0.011 468 Dihedral : 4.254 14.953 396 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.12 % Allowed : 21.18 % 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 (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: -2.68 (0.37), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.012 0.003 PHE B 94 TYR 0.006 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01748 ( 70) hydrogen bonds : angle 3.57915 ( 222) covalent geometry : bond 0.00324 ( 2784) covalent geometry : angle 0.43340 ( 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: 9 poor density : 51 time to evaluate : 0.312 Fit side-chains REVERT: B 34 LYS cc_start: 0.7604 (mttp) cc_final: 0.7122 (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: 0.7787 (ttmm) REVERT: C 43 LYS cc_start: 0.8271 (tttm) cc_final: 0.7749 (ttmm) REVERT: C 45 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8506 (tttt) REVERT: E 34 LYS cc_start: 0.7702 (mttm) cc_final: 0.7197 (mmtt) REVERT: E 43 LYS cc_start: 0.8560 (tttm) cc_final: 0.8046 (ttmt) REVERT: D 34 LYS cc_start: 0.7852 (mtmm) cc_final: 0.7312 (tmmt) REVERT: D 43 LYS cc_start: 0.8304 (tttm) cc_final: 0.7790 (ttmm) REVERT: F 43 LYS cc_start: 0.8257 (tttm) cc_final: 0.7734 (ttmm) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 1.5362 time to fit residues: 81.4756 Evaluate side-chains 60 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR 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 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=1.00 ------------------------------------------------------------------------------- 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: 10.0000 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.105457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088016 restraints weight = 3540.555| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.57 r_work: 0.3395 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2784 Z= 0.281 Angle : 0.534 4.306 3762 Z= 0.304 Chirality : 0.051 0.129 492 Planarity : 0.003 0.010 468 Dihedral : 4.799 15.915 396 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.86 % Allowed : 19.10 % 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: -2.93 (0.35), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.015 0.004 PHE B 94 TYR 0.008 0.003 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02461 ( 70) hydrogen bonds : angle 3.86372 ( 222) covalent geometry : bond 0.00620 ( 2784) covalent geometry : angle 0.53408 ( 3762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2956.01 seconds wall clock time: 51 minutes 9.26 seconds (3069.26 seconds total)