Starting phenix.real_space_refine on Sat May 10 00:58:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqv_45824/05_2025/9cqv_45824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqv_45824/05_2025/9cqv_45824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cqv_45824/05_2025/9cqv_45824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqv_45824/05_2025/9cqv_45824.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqv_45824/05_2025/9cqv_45824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqv_45824/05_2025/9cqv_45824.cif" } resolution = 2.75 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= 0.020 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 21 residue(s): 0.01s 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: 3.78, per 1000 atoms: 0.85 Number of scatterers: 4470 At special positions: 0 Unit cell: (81.585, 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: 1.14 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: 37 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 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 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: 3.554A 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 16 Processing helix chain 'B' and resid 19 through 35 removed outlier: 3.512A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.990A 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 80 through 85 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 99 through 119 removed outlier: 4.031A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.592A 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 89 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.670A 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: 3.866A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 35 removed outlier: 3.635A pdb=" N GLY D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.642A 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 50 through 56 Processing helix chain 'D' and resid 57 through 77 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: 3.982A pdb=" N PHE D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.660A 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. 978 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: 1.16 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 1629 1.38 - 1.55: 2938 1.55 - 1.72: 9 1.72 - 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 1.460 1.500 -0.041 1.21e-02 6.83e+03 1.13e+01 bond pdb=" N VAL D 23 " pdb=" CA VAL D 23 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.07e+01 bond pdb=" N VAL B 18 " pdb=" CA VAL B 18 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 8.75e+00 bond pdb=" N ASN B 80 " pdb=" CA ASN B 80 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.16e-02 7.43e+03 8.45e+00 bond pdb=" N THR C 38 " pdb=" CA THR C 38 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.43e+00 ... (remaining 4605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 5880 1.36 - 2.72: 308 2.72 - 4.08: 110 4.08 - 5.44: 29 5.44 - 6.80: 3 Bond angle restraints: 6330 Sorted by residual: angle pdb=" C PHE C 36 " pdb=" N PRO C 37 " pdb=" CA PRO C 37 " ideal model delta sigma weight residual 118.85 124.27 -5.42 1.09e+00 8.42e-01 2.47e+01 angle pdb=" CA LEU B 81 " pdb=" C LEU B 81 " pdb=" O LEU B 81 " ideal model delta sigma weight residual 120.55 116.25 4.30 1.06e+00 8.90e-01 1.65e+01 angle pdb=" N GLU D 22 " pdb=" CA GLU D 22 " pdb=" C GLU D 22 " ideal model delta sigma weight residual 111.14 115.07 -3.93 1.08e+00 8.57e-01 1.33e+01 angle pdb=" N VAL D 137 " pdb=" CA VAL D 137 " pdb=" C VAL D 137 " ideal model delta sigma weight residual 110.72 107.25 3.47 1.01e+00 9.80e-01 1.18e+01 angle pdb=" CA LYS C 40 " pdb=" C LYS C 40 " pdb=" O LYS C 40 " ideal model delta sigma weight residual 120.55 116.97 3.58 1.06e+00 8.90e-01 1.14e+01 ... (remaining 6325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 2257 15.99 - 31.98: 227 31.98 - 47.97: 93 47.97 - 63.96: 29 63.96 - 79.95: 8 Dihedral angle restraints: 2614 sinusoidal: 990 harmonic: 1624 Sorted by residual: dihedral pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " pdb=" NE ARG A 92 " pdb=" CZ ARG A 92 " ideal model delta sinusoidal sigma weight residual -90.00 -39.81 -50.19 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" C2D HEM A 201 " pdb=" C3D HEM A 201 " pdb=" CAD HEM A 201 " pdb=" CBD HEM A 201 " ideal model delta sinusoidal sigma weight residual -180.00 -100.05 -79.95 2 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" C2D HEM B 201 " pdb=" C3D HEM B 201 " pdb=" CAD HEM B 201 " pdb=" CBD HEM B 201 " ideal model delta sinusoidal sigma weight residual -0.00 -78.97 78.97 2 2.00e+01 2.50e-03 1.16e+01 ... (remaining 2611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 560 0.058 - 0.116: 100 0.116 - 0.175: 25 0.175 - 0.233: 5 0.233 - 0.291: 2 Chirality restraints: 692 Sorted by residual: 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 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 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 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL B 18 " pdb=" CA VAL B 18 " pdb=" CG1 VAL B 18 " pdb=" CG2 VAL B 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 689 not shown) Planarity restraints: 790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 40 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C LYS C 40 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS C 40 " -0.012 2.00e-02 2.50e+03 pdb=" N THR C 41 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 99 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO B 100 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 124 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.024 5.00e-02 4.00e+02 ... (remaining 787 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 419 2.74 - 3.28: 4311 3.28 - 3.82: 7885 3.82 - 4.36: 9191 4.36 - 4.90: 15788 Nonbonded interactions: 37594 Sorted by model distance: nonbonded pdb=" OG SER C 3 " pdb=" OD1 ASP C 6 " model vdw 2.206 3.040 nonbonded pdb=" OE1 GLU D 101 " pdb=" NH1 ARG D 104 " model vdw 2.266 3.120 nonbonded pdb=" OE1 GLU B 101 " pdb=" NH1 ARG B 104 " model vdw 2.272 3.120 nonbonded pdb=" O PRO A 114 " pdb=" NE2 HIS B 116 " model vdw 2.316 3.120 nonbonded pdb=" OE1 GLU C 27 " pdb=" NE2 HIS C 112 " model vdw 2.379 3.120 ... (remaining 37589 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: 2.580 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.950 Find NCS groups from input model: 0.150 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:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 0.165 4614 Z= 0.332 Angle : 0.790 6.804 6330 Z= 0.516 Chirality : 0.052 0.291 692 Planarity : 0.006 0.045 790 Dihedral : 16.702 79.948 1562 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.08 % Allowed : 16.74 % Favored : 80.18 % 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: 2.90 (0.35), residues: 558 helix: 2.48 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -0.13 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 14 HIS 0.004 0.001 HIS D 63 PHE 0.015 0.001 PHE C 36 TYR 0.009 0.002 TYR A 24 ARG 0.008 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.12235 ( 341) hydrogen bonds : angle 4.89783 ( 978) covalent geometry : bond 0.00508 ( 4610) covalent geometry : angle 0.79010 ( 6330) Misc. bond : bond 0.10715 ( 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 76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.455 Fit side-chains REVERT: A 139 LYS cc_start: 0.4413 (OUTLIER) cc_final: 0.3384 (ptpt) REVERT: A 140 TYR cc_start: -0.0282 (OUTLIER) cc_final: -0.0601 (m-80) REVERT: D 17 LYS cc_start: 0.8177 (mptp) cc_final: 0.7810 (mtpt) REVERT: D 90 GLU cc_start: 0.7980 (tt0) cc_final: 0.7328 (tp30) outliers start: 14 outliers final: 5 residues processed: 72 average time/residue: 1.4037 time to fit residues: 104.4232 Evaluate side-chains 65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 134 VAL 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: 0.6980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS B 131 GLN C 68 ASN D 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.147503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127615 restraints weight = 4527.773| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.63 r_work: 0.3431 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 4614 Z= 0.146 Angle : 0.592 7.010 6330 Z= 0.277 Chirality : 0.040 0.130 692 Planarity : 0.006 0.045 790 Dihedral : 10.350 81.503 630 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.85 % Allowed : 13.00 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.35), residues: 558 helix: 2.44 (0.24), residues: 436 sheet: None (None), residues: 0 loop : 0.34 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 14 HIS 0.005 0.001 HIS B 63 PHE 0.012 0.002 PHE B 118 TYR 0.008 0.002 TYR B 35 ARG 0.007 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 341) hydrogen bonds : angle 4.06650 ( 978) covalent geometry : bond 0.00389 ( 4610) covalent geometry : angle 0.59166 ( 6330) Misc. bond : bond 0.07021 ( 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 86 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.481 Fit side-chains REVERT: A 16 LYS cc_start: 0.7811 (tptp) cc_final: 0.7278 (mptt) REVERT: B 95 LYS cc_start: 0.7771 (tttt) cc_final: 0.7298 (mptt) REVERT: D 17 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7964 (mtpt) REVERT: D 32 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8678 (mp) REVERT: D 66 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7988 (mtmm) REVERT: D 82 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7455 (tttt) REVERT: D 90 GLU cc_start: 0.7944 (tt0) cc_final: 0.7279 (tp30) REVERT: D 134 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7373 (m) outliers start: 22 outliers final: 11 residues processed: 77 average time/residue: 1.4852 time to fit residues: 118.2074 Evaluate side-chains 77 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 79 ASP 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: 5.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 31 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN B 117 HIS B 131 GLN C 68 ASN D 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128418 restraints weight = 4539.060| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.59 r_work: 0.3419 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 4614 Z= 0.138 Angle : 0.578 6.643 6330 Z= 0.268 Chirality : 0.039 0.124 692 Planarity : 0.006 0.045 790 Dihedral : 10.091 81.302 624 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.07 % Allowed : 14.98 % 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: 3.00 (0.35), residues: 558 helix: 2.46 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 0.30 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.004 0.001 HIS B 63 PHE 0.010 0.001 PHE B 118 TYR 0.007 0.001 TYR B 35 ARG 0.006 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 341) hydrogen bonds : angle 3.94921 ( 978) covalent geometry : bond 0.00370 ( 4610) covalent geometry : angle 0.57797 ( 6330) Misc. bond : bond 0.07124 ( 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 85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.475 Fit side-chains REVERT: A 16 LYS cc_start: 0.7869 (tptp) cc_final: 0.7413 (mptt) REVERT: B 95 LYS cc_start: 0.7745 (tttt) cc_final: 0.7449 (mptt) REVERT: D 17 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8106 (mtpt) REVERT: D 66 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8029 (mtmm) REVERT: D 82 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7528 (tttt) REVERT: D 90 GLU cc_start: 0.7990 (tt0) cc_final: 0.7383 (tp30) REVERT: D 134 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7465 (m) outliers start: 23 outliers final: 10 residues processed: 75 average time/residue: 1.5569 time to fit residues: 120.3842 Evaluate side-chains 75 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 82 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: 3.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS C 9 ASN D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126581 restraints weight = 4514.456| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.59 r_work: 0.3408 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 4614 Z= 0.148 Angle : 0.591 6.805 6330 Z= 0.274 Chirality : 0.040 0.126 692 Planarity : 0.006 0.046 790 Dihedral : 9.929 82.022 622 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.96 % Allowed : 15.20 % Favored : 80.84 % 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: 2.88 (0.35), residues: 558 helix: 2.40 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 0.16 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.004 0.001 HIS B 63 PHE 0.010 0.001 PHE B 118 TYR 0.007 0.001 TYR B 35 ARG 0.006 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 341) hydrogen bonds : angle 3.96269 ( 978) covalent geometry : bond 0.00398 ( 4610) covalent geometry : angle 0.59078 ( 6330) Misc. bond : bond 0.07756 ( 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 81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7925 (tptp) cc_final: 0.7538 (mptt) REVERT: B 90 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7213 (tm-30) REVERT: B 95 LYS cc_start: 0.7742 (tttt) cc_final: 0.7461 (mptt) REVERT: D 17 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8130 (mtpt) REVERT: D 66 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8054 (mtmm) REVERT: D 82 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7547 (tttt) REVERT: D 134 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7497 (m) outliers start: 18 outliers final: 11 residues processed: 73 average time/residue: 1.4731 time to fit residues: 110.9594 Evaluate side-chains 76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 82 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: 1.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS C 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.147890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128487 restraints weight = 4609.575| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.61 r_work: 0.3425 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 4614 Z= 0.127 Angle : 0.568 6.207 6330 Z= 0.261 Chirality : 0.039 0.121 692 Planarity : 0.005 0.045 790 Dihedral : 9.765 80.616 622 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 4.63 % Allowed : 14.54 % Favored : 80.84 % 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: 3.11 (0.36), residues: 558 helix: 2.49 (0.24), residues: 442 sheet: None (None), residues: 0 loop : 0.36 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.003 0.001 HIS C 58 PHE 0.008 0.001 PHE B 118 TYR 0.006 0.001 TYR B 35 ARG 0.006 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 341) hydrogen bonds : angle 3.84647 ( 978) covalent geometry : bond 0.00346 ( 4610) covalent geometry : angle 0.56752 ( 6330) Misc. bond : bond 0.06780 ( 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 82 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.478 Fit side-chains REVERT: A 16 LYS cc_start: 0.7872 (tptp) cc_final: 0.7465 (mptt) REVERT: B 21 ASP cc_start: 0.6236 (OUTLIER) cc_final: 0.5834 (m-30) REVERT: B 90 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6849 (mt-10) REVERT: B 95 LYS cc_start: 0.7743 (tttt) cc_final: 0.7491 (mptt) REVERT: D 17 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8063 (mtpt) REVERT: D 66 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7967 (mtmm) REVERT: D 82 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7381 (tppt) REVERT: D 90 GLU cc_start: 0.7915 (tt0) cc_final: 0.7334 (tm-30) REVERT: D 134 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7381 (m) outliers start: 21 outliers final: 8 residues processed: 74 average time/residue: 1.3341 time to fit residues: 102.0336 Evaluate side-chains 72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 82 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: 0.7980 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 22 optimal weight: 0.0470 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.0050 overall best weight: 0.3070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS C 68 ASN C 122 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130386 restraints weight = 4485.885| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.63 r_work: 0.3473 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 4614 Z= 0.104 Angle : 0.537 5.470 6330 Z= 0.246 Chirality : 0.037 0.131 692 Planarity : 0.005 0.043 790 Dihedral : 9.507 79.926 622 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.64 % Allowed : 16.52 % Favored : 80.84 % 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: 3.34 (0.36), residues: 558 helix: 2.69 (0.25), residues: 438 sheet: None (None), residues: 0 loop : 0.40 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.002 0.001 HIS C 122 PHE 0.006 0.001 PHE D 118 TYR 0.006 0.001 TYR B 130 ARG 0.007 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.02844 ( 341) hydrogen bonds : angle 3.64674 ( 978) covalent geometry : bond 0.00280 ( 4610) covalent geometry : angle 0.53715 ( 6330) Misc. bond : bond 0.05210 ( 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 74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.477 Fit side-chains REVERT: A 16 LYS cc_start: 0.7838 (tptp) cc_final: 0.7431 (mptt) REVERT: B 90 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7089 (tm-30) REVERT: D 17 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7947 (mtpt) REVERT: D 82 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7344 (tppt) REVERT: D 90 GLU cc_start: 0.7882 (tt0) cc_final: 0.7294 (tm-30) REVERT: D 134 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7298 (m) outliers start: 12 outliers final: 4 residues processed: 67 average time/residue: 1.5440 time to fit residues: 106.6266 Evaluate side-chains 63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 82 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: 3.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126611 restraints weight = 4521.762| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.65 r_work: 0.3421 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 4614 Z= 0.137 Angle : 0.578 6.676 6330 Z= 0.268 Chirality : 0.040 0.128 692 Planarity : 0.006 0.045 790 Dihedral : 9.521 81.704 618 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.30 % Allowed : 16.96 % Favored : 79.74 % 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: 3.12 (0.35), residues: 558 helix: 2.56 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 0.28 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.004 0.001 HIS B 63 PHE 0.009 0.001 PHE B 118 TYR 0.006 0.001 TYR B 35 ARG 0.007 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 341) hydrogen bonds : angle 3.79817 ( 978) covalent geometry : bond 0.00371 ( 4610) covalent geometry : angle 0.57829 ( 6330) Misc. bond : bond 0.07377 ( 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 75 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.444 Fit side-chains REVERT: A 16 LYS cc_start: 0.7862 (tptp) cc_final: 0.7464 (mptt) REVERT: B 90 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6799 (mt-10) REVERT: B 101 GLU cc_start: 0.7865 (tp30) cc_final: 0.7657 (tp30) REVERT: D 17 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8035 (mtpt) REVERT: D 66 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7971 (mtmm) REVERT: D 82 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7379 (tppt) REVERT: D 90 GLU cc_start: 0.7908 (tt0) cc_final: 0.7253 (tm-30) REVERT: D 134 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7348 (m) outliers start: 15 outliers final: 6 residues processed: 68 average time/residue: 1.4293 time to fit residues: 100.4551 Evaluate side-chains 70 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 17 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS C 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126616 restraints weight = 4465.391| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.61 r_work: 0.3418 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 4614 Z= 0.145 Angle : 0.594 6.674 6330 Z= 0.276 Chirality : 0.041 0.127 692 Planarity : 0.006 0.045 790 Dihedral : 9.611 82.469 618 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.08 % Allowed : 16.96 % 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: 3.02 (0.35), residues: 558 helix: 2.47 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 0.31 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.004 0.001 HIS B 63 PHE 0.010 0.001 PHE B 118 TYR 0.007 0.001 TYR B 35 ARG 0.007 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 341) hydrogen bonds : angle 3.82125 ( 978) covalent geometry : bond 0.00391 ( 4610) covalent geometry : angle 0.59418 ( 6330) Misc. bond : bond 0.07289 ( 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 74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7896 (tptp) cc_final: 0.7536 (mptt) REVERT: D 17 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8047 (mtpt) REVERT: D 66 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7976 (mtmm) REVERT: D 82 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7375 (tppt) REVERT: D 134 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7362 (m) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 1.4861 time to fit residues: 104.2452 Evaluate side-chains 72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 82 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: 0.7980 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS C 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126462 restraints weight = 4524.685| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.62 r_work: 0.3418 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 4614 Z= 0.145 Angle : 0.595 6.707 6330 Z= 0.277 Chirality : 0.041 0.127 692 Planarity : 0.006 0.045 790 Dihedral : 9.627 82.296 618 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.64 % Allowed : 18.06 % 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: 3.08 (0.35), residues: 558 helix: 2.40 (0.24), residues: 444 sheet: None (None), residues: 0 loop : 0.66 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.004 0.001 HIS B 63 PHE 0.010 0.001 PHE B 118 TYR 0.007 0.001 TYR B 35 ARG 0.007 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 341) hydrogen bonds : angle 3.81037 ( 978) covalent geometry : bond 0.00392 ( 4610) covalent geometry : angle 0.59538 ( 6330) Misc. bond : bond 0.07342 ( 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 71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7882 (tptp) cc_final: 0.7510 (mptt) REVERT: D 17 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8021 (mtpt) REVERT: D 66 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7990 (mtmm) REVERT: D 82 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7384 (tppt) REVERT: D 134 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.7378 (m) outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 1.4567 time to fit residues: 97.7518 Evaluate side-chains 70 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 17 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS C 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126232 restraints weight = 4494.909| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.61 r_work: 0.3414 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 4614 Z= 0.144 Angle : 0.596 6.686 6330 Z= 0.277 Chirality : 0.041 0.127 692 Planarity : 0.006 0.045 790 Dihedral : 9.631 81.970 618 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.64 % Allowed : 18.06 % 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: 3.06 (0.35), residues: 558 helix: 2.39 (0.24), residues: 444 sheet: None (None), residues: 0 loop : 0.65 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.004 0.001 HIS B 63 PHE 0.010 0.001 PHE B 118 TYR 0.007 0.001 TYR B 35 ARG 0.008 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 341) hydrogen bonds : angle 3.80572 ( 978) covalent geometry : bond 0.00390 ( 4610) covalent geometry : angle 0.59556 ( 6330) Misc. bond : bond 0.07387 ( 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 71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7886 (tptp) cc_final: 0.7511 (mptt) REVERT: D 17 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8029 (mtpt) REVERT: D 66 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7985 (mtmm) REVERT: D 82 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7388 (tppt) REVERT: D 134 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7376 (m) outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 1.4438 time to fit residues: 96.9189 Evaluate side-chains 70 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 17 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS C 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126489 restraints weight = 4521.538| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.62 r_work: 0.3416 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 4614 Z= 0.140 Angle : 0.592 6.599 6330 Z= 0.276 Chirality : 0.040 0.127 692 Planarity : 0.006 0.045 790 Dihedral : 9.610 81.442 618 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.64 % Allowed : 17.84 % Favored : 79.52 % 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: 2.41 (0.24), residues: 444 sheet: None (None), residues: 0 loop : 0.67 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.004 0.001 HIS B 63 PHE 0.010 0.001 PHE B 118 TYR 0.007 0.001 TYR B 35 ARG 0.008 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 341) hydrogen bonds : angle 3.78754 ( 978) covalent geometry : bond 0.00380 ( 4610) covalent geometry : angle 0.59200 ( 6330) Misc. bond : bond 0.07258 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.69 seconds wall clock time: 58 minutes 13.88 seconds (3493.88 seconds total)