Starting phenix.real_space_refine on Sat May 10 00:59:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqw_45825/05_2025/9cqw_45825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqw_45825/05_2025/9cqw_45825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cqw_45825/05_2025/9cqw_45825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqw_45825/05_2025/9cqw_45825.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqw_45825/05_2025/9cqw_45825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqw_45825/05_2025/9cqw_45825.cif" } resolution = 2.61 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= 0.026 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 12 5.16 5 C 2900 2.51 5 N 760 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4470 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1058 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "B" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "C" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1058 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "D" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.90, per 1000 atoms: 0.87 Number of scatterers: 4470 At special positions: 0 Unit cell: (77.175, 72.765, 66.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 12 16.00 O 794 8.00 N 760 7.00 C 2900 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 524.2 milliseconds 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 88.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.500A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.699A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.613A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 35 removed outlier: 3.870A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.143A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 57 through 76 Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.962A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.709A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.590A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 35 removed outlier: 3.849A pdb=" N GLY D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.569A pdb=" N GLY D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 57 through 76 Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 95 Processing helix chain 'D' and resid 99 through 119 removed outlier: 3.964A pdb=" N PHE D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 143 341 hydrogen bonds defined for protein. 975 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: 1.18 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 1498 1.37 - 1.54: 3041 1.54 - 1.71: 37 1.71 - 1.89: 18 1.89 - 2.06: 16 Bond restraints: 4610 Sorted by residual: bond pdb=" N VAL B 23 " pdb=" CA VAL B 23 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.17e-02 7.31e+03 1.15e+01 bond pdb=" N VAL D 23 " pdb=" CA VAL D 23 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.17e-02 7.31e+03 1.06e+01 bond pdb=" N PHE D 42 " pdb=" CA PHE D 42 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.54e+00 bond pdb=" C PRO A 4 " pdb=" O PRO A 4 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.26e-02 6.30e+03 9.24e+00 bond pdb=" N VAL B 67 " pdb=" CA VAL B 67 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.81e+00 ... (remaining 4605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 5691 1.26 - 2.53: 439 2.53 - 3.79: 158 3.79 - 5.06: 30 5.06 - 6.32: 12 Bond angle restraints: 6330 Sorted by residual: angle pdb=" N GLU B 22 " pdb=" CA GLU B 22 " pdb=" C GLU B 22 " ideal model delta sigma weight residual 111.14 116.45 -5.31 1.08e+00 8.57e-01 2.41e+01 angle pdb=" N GLU D 22 " pdb=" CA GLU D 22 " pdb=" C GLU D 22 " ideal model delta sigma weight residual 111.14 115.86 -4.72 1.08e+00 8.57e-01 1.91e+01 angle pdb=" CA VAL B 23 " pdb=" C VAL B 23 " pdb=" O VAL B 23 " ideal model delta sigma weight residual 121.17 117.10 4.07 1.06e+00 8.90e-01 1.47e+01 angle pdb=" CA VAL D 23 " pdb=" C VAL D 23 " pdb=" O VAL D 23 " ideal model delta sigma weight residual 121.17 117.28 3.89 1.06e+00 8.90e-01 1.35e+01 angle pdb=" CA VAL D 20 " pdb=" C VAL D 20 " pdb=" O VAL D 20 " ideal model delta sigma weight residual 120.95 117.24 3.71 1.04e+00 9.25e-01 1.27e+01 ... (remaining 6325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 2288 17.87 - 35.74: 224 35.74 - 53.60: 81 53.60 - 71.47: 12 71.47 - 89.34: 9 Dihedral angle restraints: 2614 sinusoidal: 990 harmonic: 1624 Sorted by residual: dihedral pdb=" CA ASP C 126 " pdb=" CB ASP C 126 " pdb=" CG ASP C 126 " pdb=" OD1 ASP C 126 " ideal model delta sinusoidal sigma weight residual -30.00 -90.09 60.09 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C1A HEM C 201 " pdb=" C2A HEM C 201 " pdb=" CAA HEM C 201 " pdb=" CBA HEM C 201 " ideal model delta sinusoidal sigma weight residual 0.00 89.34 -89.34 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C1A HEM A 201 " pdb=" C2A HEM A 201 " pdb=" CAA HEM A 201 " pdb=" CBA HEM A 201 " ideal model delta sinusoidal sigma weight residual 0.00 87.43 -87.43 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 2611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 565 0.065 - 0.130: 104 0.130 - 0.195: 18 0.195 - 0.259: 3 0.259 - 0.324: 2 Chirality restraints: 692 Sorted by residual: chirality pdb=" CB VAL B 134 " pdb=" CA VAL B 134 " pdb=" CG1 VAL B 134 " pdb=" CG2 VAL B 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CB VAL D 134 " pdb=" CA VAL D 134 " pdb=" CG1 VAL D 134 " pdb=" CG2 VAL D 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VAL D 18 " pdb=" CA VAL D 18 " pdb=" CG1 VAL D 18 " pdb=" CG2 VAL D 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 689 not shown) Planarity restraints: 790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 123 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO D 124 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO B 124 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 124 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 125 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 125 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 125 " 0.022 5.00e-02 4.00e+02 ... (remaining 787 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 83 2.71 - 3.25: 4305 3.25 - 3.80: 7714 3.80 - 4.35: 9849 4.35 - 4.90: 16056 Nonbonded interactions: 38007 Sorted by model distance: nonbonded pdb=" OE1 GLU D 101 " pdb=" NH1 ARG D 104 " model vdw 2.158 3.120 nonbonded pdb=" OE1 GLU B 101 " pdb=" NH1 ARG B 104 " model vdw 2.166 3.120 nonbonded pdb=" O PRO A 114 " pdb=" NE2 HIS B 116 " model vdw 2.320 3.120 nonbonded pdb=" O PRO C 114 " pdb=" NE2 HIS D 116 " model vdw 2.352 3.120 nonbonded pdb=" OE2 GLU C 30 " pdb=" ND1 HIS C 50 " model vdw 2.373 3.120 ... (remaining 38002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 2.880 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.006 0.124 4614 Z= 0.376 Angle : 0.868 6.324 6330 Z= 0.595 Chirality : 0.057 0.324 692 Planarity : 0.006 0.048 790 Dihedral : 17.308 89.341 1562 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 5.51 % Allowed : 15.20 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.36), residues: 558 helix: 2.34 (0.25), residues: 432 sheet: None (None), residues: 0 loop : 0.25 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 15 HIS 0.006 0.001 HIS B 63 PHE 0.015 0.002 PHE A 36 TYR 0.013 0.002 TYR D 130 ARG 0.003 0.001 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.12561 ( 341) hydrogen bonds : angle 5.21394 ( 975) covalent geometry : bond 0.00585 ( 4610) covalent geometry : angle 0.86841 ( 6330) Misc. bond : bond 0.09133 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.535 Fit side-chains REVERT: A 56 LYS cc_start: 0.8077 (tttt) cc_final: 0.7312 (mptm) REVERT: A 126 ASP cc_start: 0.8067 (t70) cc_final: 0.7792 (t70) REVERT: B 90 GLU cc_start: 0.7832 (tp30) cc_final: 0.7559 (mm-30) REVERT: B 99 ASP cc_start: 0.7535 (t70) cc_final: 0.7269 (t70) REVERT: C 56 LYS cc_start: 0.8043 (tttt) cc_final: 0.7277 (mptm) REVERT: C 92 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7441 (mtt-85) REVERT: C 126 ASP cc_start: 0.8070 (t70) cc_final: 0.7780 (t70) REVERT: C 127 LYS cc_start: 0.8403 (mtpt) cc_final: 0.7890 (mtmt) REVERT: D 17 LYS cc_start: 0.8390 (mttt) cc_final: 0.7886 (mtpt) REVERT: D 22 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6546 (mm-30) REVERT: D 43 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6835 (mm-30) REVERT: D 65 LYS cc_start: 0.8509 (tttm) cc_final: 0.7953 (ttmt) REVERT: D 66 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8257 (mtmt) REVERT: D 90 GLU cc_start: 0.7605 (tt0) cc_final: 0.7164 (mm-30) REVERT: D 117 HIS cc_start: 0.7600 (t-170) cc_final: 0.6995 (m-70) REVERT: D 120 LYS cc_start: 0.7430 (mmtm) cc_final: 0.7194 (tptt) REVERT: D 139 ASN cc_start: 0.7338 (m110) cc_final: 0.7053 (m-40) outliers start: 25 outliers final: 8 residues processed: 96 average time/residue: 1.5822 time to fit residues: 156.2338 Evaluate side-chains 87 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN D 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120331 restraints weight = 4193.115| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.48 r_work: 0.3258 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 4614 Z= 0.149 Angle : 0.599 5.382 6330 Z= 0.285 Chirality : 0.041 0.126 692 Planarity : 0.006 0.049 790 Dihedral : 13.055 88.709 637 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 4.19 % Allowed : 13.88 % Favored : 81.94 % 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: 2.70 (0.35), residues: 558 helix: 2.19 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 0.47 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 14 HIS 0.004 0.001 HIS D 63 PHE 0.013 0.002 PHE D 118 TYR 0.010 0.002 TYR D 130 ARG 0.003 0.001 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 341) hydrogen bonds : angle 4.13644 ( 975) covalent geometry : bond 0.00384 ( 4610) covalent geometry : angle 0.59911 ( 6330) Misc. bond : bond 0.06331 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.485 Fit side-chains REVERT: A 56 LYS cc_start: 0.8101 (tttt) cc_final: 0.7374 (mptm) REVERT: A 126 ASP cc_start: 0.8124 (t70) cc_final: 0.7815 (t70) REVERT: B 90 GLU cc_start: 0.7955 (tp30) cc_final: 0.7684 (mm-30) REVERT: B 99 ASP cc_start: 0.7554 (t70) cc_final: 0.7256 (t70) REVERT: B 132 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8370 (mtmt) REVERT: C 56 LYS cc_start: 0.8069 (tttt) cc_final: 0.7364 (mptm) REVERT: C 92 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7529 (mtt-85) REVERT: C 126 ASP cc_start: 0.8122 (t70) cc_final: 0.7905 (t70) REVERT: C 127 LYS cc_start: 0.8438 (mtpt) cc_final: 0.7975 (mtmt) REVERT: D 17 LYS cc_start: 0.8567 (mttt) cc_final: 0.8066 (mtpt) REVERT: D 22 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6499 (mm-30) REVERT: D 26 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: D 43 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: D 65 LYS cc_start: 0.8558 (tttm) cc_final: 0.7990 (ttmt) REVERT: D 66 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8170 (mtmm) REVERT: D 82 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8323 (mptt) REVERT: D 90 GLU cc_start: 0.7681 (tt0) cc_final: 0.7177 (mm-30) REVERT: D 99 ASP cc_start: 0.7591 (t70) cc_final: 0.7271 (t70) REVERT: D 117 HIS cc_start: 0.7578 (t-170) cc_final: 0.7006 (m-70) REVERT: D 120 LYS cc_start: 0.7516 (mmtm) cc_final: 0.7250 (tptp) outliers start: 19 outliers final: 8 residues processed: 88 average time/residue: 1.5561 time to fit residues: 140.8975 Evaluate side-chains 88 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.144268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.121101 restraints weight = 4197.641| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.48 r_work: 0.3266 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4614 Z= 0.124 Angle : 0.560 5.304 6330 Z= 0.262 Chirality : 0.039 0.119 692 Planarity : 0.006 0.047 790 Dihedral : 12.569 87.904 634 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 4.19 % Allowed : 14.54 % Favored : 81.28 % 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: 3.32 (0.36), residues: 558 helix: 2.49 (0.24), residues: 422 sheet: None (None), residues: 0 loop : 1.43 (0.63), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 14 HIS 0.003 0.001 HIS A 58 PHE 0.010 0.001 PHE D 118 TYR 0.008 0.001 TYR D 130 ARG 0.002 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 341) hydrogen bonds : angle 3.92553 ( 975) covalent geometry : bond 0.00330 ( 4610) covalent geometry : angle 0.55986 ( 6330) Misc. bond : bond 0.05133 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.496 Fit side-chains REVERT: A 56 LYS cc_start: 0.8081 (tttt) cc_final: 0.7387 (mptm) REVERT: A 126 ASP cc_start: 0.8104 (t70) cc_final: 0.7827 (t70) REVERT: B 26 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: B 99 ASP cc_start: 0.7493 (t70) cc_final: 0.7190 (t70) REVERT: B 101 GLU cc_start: 0.8006 (tp30) cc_final: 0.7803 (mm-30) REVERT: B 132 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8341 (mtmt) REVERT: C 56 LYS cc_start: 0.8051 (tttt) cc_final: 0.7382 (mptm) REVERT: C 92 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7498 (mtt-85) REVERT: C 127 LYS cc_start: 0.8473 (mtpt) cc_final: 0.7966 (mtmt) REVERT: D 17 LYS cc_start: 0.8551 (mttt) cc_final: 0.8021 (mtpt) REVERT: D 22 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6474 (mm-30) REVERT: D 26 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: D 43 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: D 65 LYS cc_start: 0.8531 (tttm) cc_final: 0.7956 (ttmt) REVERT: D 66 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8166 (mtmm) REVERT: D 90 GLU cc_start: 0.7695 (tt0) cc_final: 0.7130 (mm-30) REVERT: D 95 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7609 (mttm) REVERT: D 99 ASP cc_start: 0.7529 (t70) cc_final: 0.7204 (t70) REVERT: D 117 HIS cc_start: 0.7579 (t-170) cc_final: 0.6988 (m-70) REVERT: D 120 LYS cc_start: 0.7485 (mmtm) cc_final: 0.7204 (tptt) outliers start: 19 outliers final: 8 residues processed: 84 average time/residue: 1.7033 time to fit residues: 146.9041 Evaluate side-chains 86 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.143012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119930 restraints weight = 4197.029| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.49 r_work: 0.3246 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 4614 Z= 0.139 Angle : 0.583 5.349 6330 Z= 0.275 Chirality : 0.040 0.124 692 Planarity : 0.006 0.048 790 Dihedral : 12.595 87.214 632 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 4.41 % Allowed : 14.32 % Favored : 81.28 % 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: 3.18 (0.36), residues: 558 helix: 2.41 (0.24), residues: 420 sheet: None (None), residues: 0 loop : 1.29 (0.62), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 14 HIS 0.004 0.001 HIS D 63 PHE 0.011 0.001 PHE D 118 TYR 0.007 0.001 TYR C 140 ARG 0.002 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 341) hydrogen bonds : angle 3.93774 ( 975) covalent geometry : bond 0.00366 ( 4610) covalent geometry : angle 0.58271 ( 6330) Misc. bond : bond 0.05792 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.447 Fit side-chains REVERT: A 56 LYS cc_start: 0.8072 (tttt) cc_final: 0.7322 (mptm) REVERT: A 126 ASP cc_start: 0.8066 (t70) cc_final: 0.7713 (t70) REVERT: B 26 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: B 99 ASP cc_start: 0.7522 (t70) cc_final: 0.7197 (t70) REVERT: B 132 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8365 (mtmt) REVERT: C 56 LYS cc_start: 0.8037 (tttt) cc_final: 0.7332 (mptm) REVERT: C 92 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7463 (mtt-85) REVERT: C 127 LYS cc_start: 0.8453 (mtpt) cc_final: 0.7924 (mtmt) REVERT: D 17 LYS cc_start: 0.8596 (mttt) cc_final: 0.8009 (mtpt) REVERT: D 22 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6366 (mm-30) REVERT: D 26 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: D 43 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: D 65 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7928 (ttmt) REVERT: D 66 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8176 (mtmm) REVERT: D 90 GLU cc_start: 0.7678 (tt0) cc_final: 0.7054 (mm-30) REVERT: D 95 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7550 (mttm) REVERT: D 99 ASP cc_start: 0.7551 (t70) cc_final: 0.7192 (t70) REVERT: D 117 HIS cc_start: 0.7550 (t-170) cc_final: 0.6949 (m-70) REVERT: D 120 LYS cc_start: 0.7470 (mmtm) cc_final: 0.7091 (tptt) outliers start: 20 outliers final: 6 residues processed: 87 average time/residue: 1.6160 time to fit residues: 144.4663 Evaluate side-chains 85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.141781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118951 restraints weight = 4264.839| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.48 r_work: 0.3234 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 4614 Z= 0.153 Angle : 0.599 5.448 6330 Z= 0.284 Chirality : 0.041 0.127 692 Planarity : 0.006 0.049 790 Dihedral : 12.403 86.202 630 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.96 % Allowed : 14.98 % Favored : 81.06 % 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: 3.01 (0.35), residues: 558 helix: 2.32 (0.24), residues: 420 sheet: None (None), residues: 0 loop : 1.13 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 14 HIS 0.004 0.001 HIS D 116 PHE 0.011 0.002 PHE D 118 TYR 0.008 0.001 TYR C 140 ARG 0.002 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 341) hydrogen bonds : angle 3.98597 ( 975) covalent geometry : bond 0.00400 ( 4610) covalent geometry : angle 0.59878 ( 6330) Misc. bond : bond 0.06355 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.493 Fit side-chains REVERT: A 56 LYS cc_start: 0.8125 (tttt) cc_final: 0.7390 (mptm) REVERT: A 126 ASP cc_start: 0.8125 (t70) cc_final: 0.7783 (t70) REVERT: B 26 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: B 90 GLU cc_start: 0.8045 (tp30) cc_final: 0.7831 (mm-30) REVERT: B 99 ASP cc_start: 0.7556 (t70) cc_final: 0.7236 (t70) REVERT: B 132 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8381 (mtmt) REVERT: C 56 LYS cc_start: 0.8093 (tttt) cc_final: 0.7399 (mptm) REVERT: C 92 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7501 (mtt-85) REVERT: C 127 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7918 (mtmt) REVERT: D 17 LYS cc_start: 0.8653 (mttt) cc_final: 0.8065 (mtpt) REVERT: D 22 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6577 (mm-30) REVERT: D 26 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: D 43 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: D 65 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8009 (ttmt) REVERT: D 66 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8221 (mtmm) REVERT: D 90 GLU cc_start: 0.7714 (tt0) cc_final: 0.7098 (mm-30) REVERT: D 95 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7599 (mttm) REVERT: D 99 ASP cc_start: 0.7593 (t70) cc_final: 0.7245 (t70) REVERT: D 117 HIS cc_start: 0.7596 (t-170) cc_final: 0.7043 (m-70) REVERT: D 120 LYS cc_start: 0.7513 (mmtm) cc_final: 0.7148 (tptt) outliers start: 18 outliers final: 6 residues processed: 84 average time/residue: 1.5257 time to fit residues: 131.8748 Evaluate side-chains 85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.151332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131187 restraints weight = 4208.510| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.36 r_work: 0.3355 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4614 Z= 0.126 Angle : 0.561 5.315 6330 Z= 0.264 Chirality : 0.039 0.122 692 Planarity : 0.006 0.047 790 Dihedral : 12.121 86.456 630 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.52 % Allowed : 15.42 % Favored : 81.06 % 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: 3.18 (0.36), residues: 558 helix: 2.45 (0.24), residues: 420 sheet: None (None), residues: 0 loop : 1.15 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 14 HIS 0.003 0.001 HIS D 116 PHE 0.009 0.001 PHE D 118 TYR 0.007 0.001 TYR B 130 ARG 0.002 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 341) hydrogen bonds : angle 3.90882 ( 975) covalent geometry : bond 0.00334 ( 4610) covalent geometry : angle 0.56082 ( 6330) Misc. bond : bond 0.05241 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.497 Fit side-chains REVERT: A 56 LYS cc_start: 0.7962 (tttt) cc_final: 0.7291 (mptm) REVERT: A 126 ASP cc_start: 0.8168 (t70) cc_final: 0.7848 (t70) REVERT: B 26 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: B 99 ASP cc_start: 0.7494 (t70) cc_final: 0.7160 (t70) REVERT: B 132 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8315 (mtmt) REVERT: C 56 LYS cc_start: 0.7987 (tttt) cc_final: 0.7294 (mptm) REVERT: C 92 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7483 (mtt-85) REVERT: C 127 LYS cc_start: 0.8516 (mtpt) cc_final: 0.7954 (mtmt) REVERT: D 17 LYS cc_start: 0.8653 (mttt) cc_final: 0.8085 (mtpt) REVERT: D 22 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: D 26 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: D 43 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: D 65 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7974 (ttmt) REVERT: D 66 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8182 (mtmm) REVERT: D 90 GLU cc_start: 0.7675 (tt0) cc_final: 0.7053 (mm-30) REVERT: D 95 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7638 (mttm) REVERT: D 99 ASP cc_start: 0.7548 (t70) cc_final: 0.7205 (t70) REVERT: D 117 HIS cc_start: 0.7581 (t-170) cc_final: 0.7055 (m-70) REVERT: D 120 LYS cc_start: 0.7563 (mmtm) cc_final: 0.7177 (tptt) outliers start: 16 outliers final: 7 residues processed: 84 average time/residue: 1.5032 time to fit residues: 130.1132 Evaluate side-chains 89 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 0.0010 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7788 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.150575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132059 restraints weight = 4241.495| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.21 r_work: 0.3349 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4614 Z= 0.137 Angle : 0.577 5.340 6330 Z= 0.272 Chirality : 0.040 0.124 692 Planarity : 0.006 0.048 790 Dihedral : 12.126 86.935 630 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.96 % Allowed : 15.42 % Favored : 80.62 % 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: 3.09 (0.36), residues: 558 helix: 2.38 (0.24), residues: 420 sheet: None (None), residues: 0 loop : 1.12 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 14 HIS 0.004 0.001 HIS D 116 PHE 0.010 0.001 PHE D 118 TYR 0.007 0.001 TYR B 130 ARG 0.003 0.001 ARG D 104 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 341) hydrogen bonds : angle 3.95560 ( 975) covalent geometry : bond 0.00362 ( 4610) covalent geometry : angle 0.57655 ( 6330) Misc. bond : bond 0.05897 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.491 Fit side-chains REVERT: A 56 LYS cc_start: 0.8060 (tttt) cc_final: 0.7456 (mptm) REVERT: A 126 ASP cc_start: 0.8225 (t70) cc_final: 0.7894 (t70) REVERT: B 26 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: B 99 ASP cc_start: 0.7515 (t70) cc_final: 0.7207 (t70) REVERT: B 132 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8329 (mtmt) REVERT: C 56 LYS cc_start: 0.8094 (tttt) cc_final: 0.7457 (mptm) REVERT: C 92 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7580 (mtt-85) REVERT: C 127 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8065 (mtmt) REVERT: D 17 LYS cc_start: 0.8748 (mttt) cc_final: 0.8209 (mtpt) REVERT: D 22 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: D 26 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: D 43 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: D 65 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8109 (ttmt) REVERT: D 66 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8240 (mtmm) REVERT: D 90 GLU cc_start: 0.7753 (tt0) cc_final: 0.7182 (mm-30) REVERT: D 95 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7715 (mttm) REVERT: D 117 HIS cc_start: 0.7641 (t-170) cc_final: 0.7193 (m-70) REVERT: D 120 LYS cc_start: 0.7568 (mmtm) cc_final: 0.7266 (tptt) outliers start: 18 outliers final: 8 residues processed: 86 average time/residue: 1.4647 time to fit residues: 129.7368 Evaluate side-chains 89 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.151847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133501 restraints weight = 4212.959| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.19 r_work: 0.3362 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4614 Z= 0.126 Angle : 0.560 5.302 6330 Z= 0.264 Chirality : 0.039 0.121 692 Planarity : 0.006 0.047 790 Dihedral : 11.921 87.154 630 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.30 % Allowed : 16.08 % Favored : 80.62 % 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: 3.21 (0.36), residues: 558 helix: 2.47 (0.24), residues: 420 sheet: None (None), residues: 0 loop : 1.17 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 14 HIS 0.003 0.001 HIS D 116 PHE 0.009 0.001 PHE D 118 TYR 0.007 0.001 TYR B 130 ARG 0.004 0.001 ARG D 104 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 341) hydrogen bonds : angle 3.91557 ( 975) covalent geometry : bond 0.00335 ( 4610) covalent geometry : angle 0.55976 ( 6330) Misc. bond : bond 0.05422 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.480 Fit side-chains REVERT: A 56 LYS cc_start: 0.8062 (tttt) cc_final: 0.7456 (mptm) REVERT: A 126 ASP cc_start: 0.8236 (t70) cc_final: 0.7946 (t70) REVERT: B 26 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: B 99 ASP cc_start: 0.7465 (t70) cc_final: 0.7149 (t70) REVERT: C 56 LYS cc_start: 0.8090 (tttt) cc_final: 0.7462 (mptm) REVERT: C 92 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7576 (mtt-85) REVERT: C 127 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8071 (mtmt) REVERT: D 17 LYS cc_start: 0.8718 (mttt) cc_final: 0.8186 (mtpt) REVERT: D 22 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: D 26 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: D 43 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: D 65 LYS cc_start: 0.8621 (tttm) cc_final: 0.8087 (ttmt) REVERT: D 66 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8236 (mtmm) REVERT: D 90 GLU cc_start: 0.7741 (tt0) cc_final: 0.7183 (mm-30) REVERT: D 95 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7727 (mttm) REVERT: D 117 HIS cc_start: 0.7621 (t-170) cc_final: 0.7192 (m-70) REVERT: D 120 LYS cc_start: 0.7649 (mmtm) cc_final: 0.7366 (tptt) outliers start: 15 outliers final: 8 residues processed: 83 average time/residue: 1.4257 time to fit residues: 121.9402 Evaluate side-chains 90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.150470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131791 restraints weight = 4231.576| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.21 r_work: 0.3337 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4614 Z= 0.149 Angle : 0.593 5.450 6330 Z= 0.280 Chirality : 0.041 0.126 692 Planarity : 0.006 0.048 790 Dihedral : 12.116 87.535 630 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.52 % Allowed : 16.08 % Favored : 80.40 % 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: 3.01 (0.35), residues: 558 helix: 2.30 (0.24), residues: 420 sheet: None (None), residues: 0 loop : 1.19 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 14 HIS 0.004 0.001 HIS D 116 PHE 0.011 0.002 PHE D 118 TYR 0.007 0.001 TYR B 130 ARG 0.006 0.001 ARG D 104 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 341) hydrogen bonds : angle 4.00364 ( 975) covalent geometry : bond 0.00388 ( 4610) covalent geometry : angle 0.59302 ( 6330) Misc. bond : bond 0.06425 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.500 Fit side-chains REVERT: A 56 LYS cc_start: 0.8100 (tttt) cc_final: 0.7474 (mptm) REVERT: A 126 ASP cc_start: 0.8237 (t70) cc_final: 0.7910 (t70) REVERT: B 26 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: B 99 ASP cc_start: 0.7518 (t70) cc_final: 0.7198 (t70) REVERT: C 56 LYS cc_start: 0.8120 (tttt) cc_final: 0.7474 (mptm) REVERT: C 92 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7585 (mtt-85) REVERT: C 127 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8085 (mtmt) REVERT: D 17 LYS cc_start: 0.8717 (mttt) cc_final: 0.8179 (mtpt) REVERT: D 22 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: D 26 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: D 43 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: D 65 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8136 (ttmt) REVERT: D 66 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8292 (mtmm) REVERT: D 90 GLU cc_start: 0.7768 (tt0) cc_final: 0.7198 (mm-30) REVERT: D 95 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7717 (mttm) REVERT: D 117 HIS cc_start: 0.7659 (t-170) cc_final: 0.7207 (m-70) REVERT: D 120 LYS cc_start: 0.7617 (mmtm) cc_final: 0.7318 (tptt) outliers start: 16 outliers final: 8 residues processed: 83 average time/residue: 1.4789 time to fit residues: 126.5077 Evaluate side-chains 88 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.152388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.132963 restraints weight = 4191.382| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.33 r_work: 0.3382 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4614 Z= 0.115 Angle : 0.544 5.267 6330 Z= 0.255 Chirality : 0.038 0.119 692 Planarity : 0.006 0.047 790 Dihedral : 11.733 86.932 630 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.64 % Allowed : 17.40 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.36), residues: 558 helix: 2.50 (0.24), residues: 422 sheet: None (None), residues: 0 loop : 1.29 (0.62), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 14 HIS 0.003 0.001 HIS D 116 PHE 0.008 0.001 PHE D 118 TYR 0.007 0.001 TYR B 130 ARG 0.006 0.001 ARG D 104 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 341) hydrogen bonds : angle 3.88086 ( 975) covalent geometry : bond 0.00307 ( 4610) covalent geometry : angle 0.54382 ( 6330) Misc. bond : bond 0.04645 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.448 Fit side-chains REVERT: A 56 LYS cc_start: 0.7963 (tttt) cc_final: 0.7300 (mptm) REVERT: A 126 ASP cc_start: 0.8156 (t70) cc_final: 0.7904 (t70) REVERT: B 26 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7226 (mm-30) REVERT: B 99 ASP cc_start: 0.7365 (t70) cc_final: 0.7028 (t70) REVERT: C 56 LYS cc_start: 0.7977 (tttt) cc_final: 0.7280 (mptm) REVERT: C 92 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7499 (mtt-85) REVERT: C 127 LYS cc_start: 0.8516 (mtpt) cc_final: 0.7966 (mtmt) REVERT: D 17 LYS cc_start: 0.8646 (mttt) cc_final: 0.8078 (mtpt) REVERT: D 22 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: D 26 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: D 43 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: D 65 LYS cc_start: 0.8572 (tttm) cc_final: 0.8006 (ttmt) REVERT: D 90 GLU cc_start: 0.7680 (tt0) cc_final: 0.7049 (mm-30) REVERT: D 95 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7678 (mttm) REVERT: D 99 ASP cc_start: 0.7388 (t70) cc_final: 0.7054 (t70) REVERT: D 117 HIS cc_start: 0.7559 (t-170) cc_final: 0.7058 (m-70) REVERT: D 120 LYS cc_start: 0.7597 (mmtm) cc_final: 0.7314 (tptt) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 1.5145 time to fit residues: 131.0332 Evaluate side-chains 85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.151701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133410 restraints weight = 4253.685| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.20 r_work: 0.3365 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4614 Z= 0.127 Angle : 0.562 5.324 6330 Z= 0.264 Chirality : 0.040 0.123 692 Planarity : 0.006 0.048 790 Dihedral : 11.840 87.532 630 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.42 % Allowed : 17.62 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.36), residues: 558 helix: 2.42 (0.24), residues: 422 sheet: None (None), residues: 0 loop : 1.33 (0.62), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 14 HIS 0.003 0.001 HIS D 116 PHE 0.009 0.001 PHE D 118 TYR 0.007 0.001 TYR B 130 ARG 0.010 0.001 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 341) hydrogen bonds : angle 3.90870 ( 975) covalent geometry : bond 0.00336 ( 4610) covalent geometry : angle 0.56181 ( 6330) Misc. bond : bond 0.05539 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3812.23 seconds wall clock time: 66 minutes 18.72 seconds (3978.72 seconds total)